Mercurial > repos > galaxyp > phosphopeptide_kinase_mapping

annotate PhosphoPeptide_Upstream_Kinase_Mapping.pl @ 0:56658e35798d draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
author galaxyp
date Thu, 04 Nov 2021 19:37:36 +0000
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56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
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1 #!/usr/local/bin/perl
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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2
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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3 use Getopt::Std;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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4
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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5 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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6 # perl Kinase_enrichment_analysis_complete_v0.pl
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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7 #
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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8 # Nick Graham, USC
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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9 # 2016-02-27
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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10 #
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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11 # Built from scripts written by NG at UCLA in Tom Graeber's lab:
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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12 # CombinePhosphoSites.pl
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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13 # Retrieve_p_motifs.pl
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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14 # NetworKIN_Motif_Finder_v7.pl
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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15 #
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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16 # Given a list of phospho-peptides, find protein information and upstream kinases.
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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17 # Output file can be used for KS enrichment score calculations using Enrichment_Score4Directory.pl
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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18 #
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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19 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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21 my ($file_in, $average_or_sum, $file_out, $phospho_type);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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22 my ($fasta_in, $networkin_in, $motifs_in, $PhosphoSite_in, $PhosphoSite_molecular_function);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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23
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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24 ##########
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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25 ## opts ##
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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26 ##########
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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27 ## input files
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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28 # i : path to input outputfile_STEP2.txt
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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29 # f : path to fasta
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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30 # n : path to NetworKIN_201612_cutoffscore2.0.txt
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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31 # m : path to pSTY_Motifs.txt
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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32 # p : path to 2017-03_PSP_Kinase_Substrate_Dataset.txt
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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33 # r : path to 2017-03_PSP_Regulatory_sites.txt
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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34 ## options
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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35 # P : phospho_type
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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36 # F : function
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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37 ## output files
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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38 # o : path to output file
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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39
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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40 sub usage()
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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41 {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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42 print STDERR <<"EOH";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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43 This program given a list of phospho-peptides, finds protein information and upstream kinases.
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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44 usage: $0 [-hvd] [-f file]
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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45 -h : this (help) message
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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46 -i : path to input outputfile_STEP2.txt
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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47 -f : path to fasta
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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48 -n : path to NetworKIN_201612_cutoffscore2.0.txt
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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49 -m : path to pSTY_Motifs.txt
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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50 -p : path to 2017-03_PSP_Kinase_Substrate_Dataset.txt
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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51 -r : path to 2017-03_PSP_Regulatory_sites.txt
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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52 -P : phospho_type
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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53 -F : function
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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54 -o : path to output file
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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55 example: $0
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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56 EOH
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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57 exit;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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58 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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59
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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60 my %opts;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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61 getopts('i:f:n:m:p:r:o:P:F:h', \%opts) ;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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62
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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63 if (exists($opts{'h'})) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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64 usage();
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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65 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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66 if (!exists($opts{'i'}) || !-e $opts{'i'}) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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67 die('Input File not found');
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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68 } else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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69 $file_in = $opts{'i'};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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70 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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71 if (!exists($opts{'f'}) || !-e $opts{'f'}) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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72 die('Input Fasta File not found');
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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73 } else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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74 $fasta_in = $opts{'f'};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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75 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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76 if (!exists($opts{'n'}) || !-e $opts{'n'}) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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77 die('Input NetworKIN File not found');
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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78 } else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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79 $networkin_in = $opts{'n'};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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80 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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81 if (!exists($opts{'m'}) || !-e $opts{'m'}) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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82 die('Input pSTY_Motifs File not found');
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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diff changeset
83 } else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
84 $motifs_in = $opts{'m'};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
85 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
86 if (!exists($opts{'p'}) || !-e $opts{'p'}) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
87 die('Input PSP_Kinase_Substrate_Dataset File not found');
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
88 } else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
89 $PhosphoSite_in = $opts{'p'};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
90 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
91 if (!exists($opts{'r'}) || !-e $opts{'r'}) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
92 die('Input PSP_Regulatory_sites File not found');
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
93 } else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
94 $PhosphoSite_molecular_function = $opts{'r'};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
95 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
96 if (exists($opts{'P'})) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
97 $phospho_type = $opts{'P'};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
98 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
99 else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
100 $phospho_type = "sty";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
101 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
102 if (exists($opts{'F'})) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
103 $average_or_sum = $opts{'F'};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
104 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
105 else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
106 $average_or_sum = "sum";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
107 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
108 if (exists($opts{'o'})) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
109 $file_out = $opts{'o'};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
110 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
111 else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
112 $file_out = "output.tsv";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
113 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
114
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
115
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
116 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
117 # Print the relevant file names to the screen
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
118 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
119 # print "\nData file: $data_in\nFASTA file: $fasta_in\nSpecies: $species\nOutput file: $motifs_out\n\n";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
120 print "\nData file: $file_in\nAverage or sum identical p-sites? $average_or_sum\nOutput file: $file_out\n\n";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
121 print "Motifs file: $motifs_in\nNetworKIN file: networkin_in\nPhosphosite kinase substrate data: $PhosphoSite_in\nPhosphosite functional data: $PhosphoSite_molecular_function\nFASTA file: $fasta_in\n\n";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
122
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
123
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
124 print "\nPhospho-residues(s) = $phospho_type\n";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
125 if ($phospho_type ne 'y') {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
126 if ($phospho_type ne 'sty') {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
127 die "\nUsage error:\nYou must choose a phospho-type, either y or sty\n\n";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
128 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
129 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
130
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
131 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
132 # read the input data file
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
133 # average or sum identical phospho-sites, depending on the value of $average_or_sum
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
134 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
135
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
136 open (IN, "$file_in") or die "I couldn't find the input file: $file_in\n";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
137
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
138 die "\n\nScript died: You must choose either average or sum for \$average_or_sum\n\n" if (($average_or_sum ne "sum") && ($average_or_sum ne "average")) ;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
139
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
140
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
141 my (@samples, %data, @tmp_data, %n);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
142 my $line = 0;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
143
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
144 while (<IN>) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
145 chomp;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
146 my @x = split(/\t/);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
147 for my $n (0 .. $#x) {$x[$n] =~ s/\r//g; $x[$n] =~ s/\n//g; $x[$n] =~ s/\"//g;}
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
148
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
149 # Read in the samples
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
150 if ($line == 0) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
151 for my $n (1 .. $#x) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
152 push (@samples, $x[$n]);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
153 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
154 $line++;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
155 } else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
156 # check whether we have already seen a phospho-peptide
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
157 if (exists($data{$x[0]})) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
158 if ($average_or_sum eq "sum") { # add the data
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
159 # unload the data
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
160 @tmp_data = (); foreach (@{$data{$x[0]}}) { push(@tmp_data, $_); }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
161 # add the new data and repack
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
162 for my $k (0 .. $#tmp_data) { $tmp_data[$k] = $tmp_data[$k] + $x[$k+1]; }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
163 $all_data{$x[0]} = (); for my $k (0 .. $#tmp_data) { push(@{$all_data{$x[0]}}, $tmp_data[$k]); }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
164
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
165 } elsif ($average_or_sum eq "average") { # average the data
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
166 # unload the data
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
167 @tmp_data = (); foreach (@{$all_data{$x[0]}}) { push(@tmp_data, $_); }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
168 # average with the new data and repack
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
169 for my $k (0 .. $#tmp_data) { $tmp_data[$k] = ( $tmp_data[$k]*$n{$x[0]} + $x[0] ) / ($n{$x[0]} + 1); }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
170 $n{$x[0]}++;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
171 $data{$x[0]} = (); for my $k (0 .. $#tmp_data) { push(@{$data{$x[0]}}, $tmp_data[$k]); }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
172 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
173 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
174 # if the phospho-sequence has not been seen, save the data
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
175 else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
176 for my $k (1 .. $#x) { push(@{$data{$x[0]}}, $x[$k]); }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
177 $n{$x[0]} = 1;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
178 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
179 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
180 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
181 close(IN);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
182
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
183
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
184 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
185 # Search the FASTA database for phospho-sites and motifs
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
186 #
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
187 # based on Retrieve_p_peptide_motifs_v2.pl
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
188 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
189
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
190
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
191 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
192 #
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
193 # Read in the Data file:
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
194 # 1) make @p_peptides array as in the original file
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
195 # 2) make @non_p_peptides array w/o residue modifications (p, #, other)
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
196 #
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
197 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
198
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
199 my (@p_peptides, @non_p_peptides);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
200 foreach my $peptide (keys %data) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
201 $peptide =~ s/s/pS/g; $peptide =~ s/t/pT/g; $peptide =~ s/y/pY/g;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
202 push (@p_peptides, $peptide);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
203 $peptide =~ s/p//g;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
204 push(@non_p_peptides, $peptide);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
205 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
206
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
207 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
208 #
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
209 # Read in the FASTA sequence file, save them to the @sequences array
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
210 #
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
211 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
212
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
213 open (IN1, "$fasta_in") or die "I couldn't find $fasta_in\n";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
214
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
215 my (@accessions, @names, @sequences);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
216
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
217 print "Reading FASTA file $fasta_in\n";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
218 while (<IN1>) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
219 chomp;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
220 my (@x) = split(/\|/);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
221 for my $i (0 .. $#x) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
222 $x[$i] =~ s/\r//g; $x[$i] =~ s/\n//g; $x[$i] =~ s/\"//g; }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
223 if ($x[0] =~ /^>/) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
224 $x[0] =~ s/\>//g;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
225 push (@names, $x[2]);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
226 push (@accessions, $x[1]);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
227 } elsif ($x[0] =~ /^\w/) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
228 $sequences[$#accessions] = $sequences[$#accessions].$x[0];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
229 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
230 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
231 close IN1;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
232 print "Done Reading FASTA file $fasta_in\n\n";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
233
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
234
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
235 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
236 #
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
237 # Match the non_p_peptides to the @sequences array:
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
238 # 1) Format the motifs +/- 10 residues around the phospho-site
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
239 # 2) Print the original data plus the phospho-motif to the output file
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
240 #
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
241 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
242
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
243 print OUT "$headers\tFormatted Motifs\tUnique Motifs\tPhospho-site(s)\tAccessions(s)\tName(s)\n";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
244
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
245 my (%matched_sequences, %accessions, %names, %sites, @tmp_matches, @tmp_accessions, @tmp_names, @tmp_sites);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
246
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
247 for my $j (0 .. $#p_peptides) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
248 @tmp_matches = (); @tmp_accessions = (); @tmp_names = (); @tmp_sites = ();
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
249
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
250 #Find the matching protein sequence(s) for the peptide
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
251 my $site = -1; my $match = 0;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
252 for my $k (0 .. $#sequences) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
253 $site = index($sequences[$k], $non_p_peptides[$j]);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
254 if ($site != -1) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
255 push(@tmp_matches, $sequences[$k]);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
256 push(@tmp_accessions, $accessions[$k]);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
257 push(@tmp_names, $names[$k]);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
258 push(@tmp_sites, $site);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
259 $site = -1; $match++;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
260 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
261 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
262
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
263 if ($match == 0) { # Check to see if no match was found. Skip to next if no match found.
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
264 print "Warning: Failed match for $p_peptides[$j]\n";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
265 $matched_sequences{$p_peptides[$j]} = "Failed match";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
266 next;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
267 } else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
268 $matched_sequences{$p_peptides[$j]} = [ @tmp_matches ];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
269 $accessions{$p_peptides[$j]} = [ @tmp_accessions ];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
270 $names{$p_peptides[$j]} = [ @tmp_names ];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
271 $sites{$p_peptides[$j]} = [ @tmp_sites ];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
272 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
273 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
274
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
275 my (%p_residues, @tmp_p_residues, @p_sites, $left, $right, %p_motifs, @tmp_motifs_array, $tmp_motif, $tmp_site, %residues);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
276
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
277 for my $peptide_to_match ( keys %matched_sequences ) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
278 next if ($peptide_to_match eq "Failed match");
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
279 my @matches = @{$matched_sequences{$peptide_to_match}};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
280 @tmp_motifs_array = ();
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
281 for my $i (0 .. $#matches) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
282
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
283 # Find the location of the phospo-site in the sequence(s)
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
284 $tmp_site = 0; my $offset = 0;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
285 my $tmp_p_peptide = $peptide_to_match;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
286 $tmp_p_peptide =~ s/#//g; $tmp_p_peptide =~ s/\d//g; $tmp_p_peptide =~ s/\_//g; $tmp_p_peptide =~ s/\.//g;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
287
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
288 # Find all phosphorylated residues in the p_peptide
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
289 @p_sites = ();
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
290 while ($tmp_site != -1) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
291 $tmp_site = index($tmp_p_peptide, 'p', $offset);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
292 if ($tmp_site != -1) {push (@p_sites, $tmp_site);}
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
293 $offset = $tmp_site + 1;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
294 $tmp_p_peptide =~ s/p//;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
295 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
296
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
297 @tmp_p_residues = ();
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
298 for my $l (0 .. $#p_sites) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
299 push (@tmp_p_residues, $p_sites[$l]+$sites{$peptide_to_match}[$i]);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
300
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
301 # Match the sequences around the phospho residues to find the motifs
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
302 my ($desired_residues_L, $desired_residues_R);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
303 if ($tmp_p_residues[0] - 10 < 0) { #check to see if there are fewer than 10 residues left of the first p-site
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
304 # eg, XXXpYXX want $desired_residues_L = 3, $p_residues[0] = 3
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
305 $desired_residues_L = $tmp_p_residues[0];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
306 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
307 else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
308 $desired_residues_L = 10;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
309 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
310 my $seq_length = length($matched_sequences{$peptide_to_match}[$i]);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
311 if ($tmp_p_residues[$#tmp_p_residues] + 10 > $seq_length) { #check to see if there are fewer than 10 residues right of the last p-site
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
312 $desired_residues_R = $seq_length - ($tmp_p_residues[$#tmp_p_residues] + 1);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
313 # eg, XXXpYXX want $desired_residues_R = 2, $seq_length = 6, $p_residues[$#p_residues] = 3
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
314 # print "Line 170: seq_length = $seq_length\tp_residue = $p_residues[$#p_residues]\n";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
315 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
316 else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
317 $desired_residues_R = 10;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
318 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
319
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
320 my $total_length = $desired_residues_L + $tmp_p_residues[$#tmp_p_residues] - $tmp_p_residues[0] + $desired_residues_R + 1;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
321 $tmp_motif = substr($matched_sequences{$peptide_to_match}[$i], $tmp_p_residues[0] - $desired_residues_L, $total_length);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
322
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
323 # Put the "p" back in front of the appropriate phospho-residue(s).
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
324 my (@tmp_residues, $tmp_position);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
325 for my $m (0 .. $#p_sites) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
326 # print "Line 183: $p_sites[$m]\n";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
327 if ($m == 0) {$tmp_position = $desired_residues_L;}
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
328 else {$tmp_position = $desired_residues_L + $p_sites[$m] - $p_sites[0];}
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
329 # print "Line 187: p_sites = $p_sites[$m]\ttmp_position = $tmp_position\n";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
330 push (@tmp_residues, substr($tmp_motif, $tmp_position, 1));
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
331 if ($tmp_residues[$m] eq "S") {substr($tmp_motif, $tmp_position, 1, "s");}
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
332 if ($tmp_residues[$m] eq "T") {substr($tmp_motif, $tmp_position, 1, "t");}
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
333 if ($tmp_residues[$m] eq "Y") {substr($tmp_motif, $tmp_position, 1, "y");}
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
334 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
335
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
336 $tmp_motif =~ s/s/pS/g; $tmp_motif =~ s/t/pT/g; $tmp_motif =~ s/y/pY/g;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
337
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
338 # Comment out on 8.10.13 to remove the numbers from motifs
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
339 my $left_residue = $tmp_p_residues[0] - $desired_residues_L+1;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
340 my $right_residue = $tmp_p_residues[$#tmp_p_residues] + $desired_residues_R+1;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
341 $tmp_motif = $left_residue."-[ ".$tmp_motif." ]-".$right_residue;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
342 push(@tmp_motifs_array, $tmp_motif);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
343 $residues{$peptide_to_match}{$i} = [ @tmp_residues ];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
344 $p_residues{$peptide_to_match}{$i} = [ @tmp_p_residues ];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
345 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
346 $p_motifs{$peptide_to_match} = [ @tmp_motifs_array ];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
347 } ### this bracket could be in the wrong place
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
348 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
349
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
350
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
351 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
352 #
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
353 # Annotate the peptides with the NetworKIN predictions and HPRD / Phosida kinase motifs
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
354 #
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
355 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
356
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
357
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
358
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
359 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
360 #
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
361 # Read the NetworKIN_predictions file:
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
362 # 1) make a "kinases_observed" array
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
363 # 2) annotate the phospho-substrates with the appropriate kinase
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
364 #
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
365 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
366
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
367 my (@kinases_observed, $kinases);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
368 my ($p_sequence_kinase, $p_sequence, $kinase);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
369
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
370 open (IN1, "$networkin_in") or die "I couldn't find $networkin_in\n";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
371 print "\nReading the NetworKIN data: $networkin_in\n";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
372 while (<IN1>) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
373 chomp;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
374 my (@x) = split(/\t/);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
375 for my $i (0 .. $#x) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
376 $x[$i] =~ s/\r//g; $x[$i] =~ s/\n//g; $x[$i] =~ s/\"//g;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
377 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
378 next if ($x[0] eq "#substrate");
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
379 if (exists ($kinases -> {$x[2]})) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
380 #do nothing
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
381 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
382 else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
383 $kinases -> {$x[2]} = $x[2];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
384 push (@kinases_observed, $x[2]);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
385 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
386 my $tmp = $x[10]."_".$x[2]; #eg, REEILsEMKKV_PKCalpha
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
387 if (exists($p_sequence_kinase -> {$tmp})) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
388 #do nothing
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
389 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
390 else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
391 $p_sequence_kinase -> {$tmp} = $tmp;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
392 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
393 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
394 close IN1;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
395
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
396 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
397 #
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
398 # Read the Kinase motifs file:
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
399 # 1) make a "motif_sequence" array
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
400 #
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
401 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
402
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
403 my (@motif_sequence, %motif_type, %motif_count);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
404
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
405 open (IN2, "$motifs_in") or die "I couldn't find $motifs_in\n";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
406 print "Reading the Motifs file: $motifs_in\n";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
407
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
408 while (<IN2>) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
409 chomp;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
410 my (@x) = split(/\t/);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
411 for my $i (0 .. 2) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
412 $x[$i] =~ s/\r//g;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
413 $x[$i] =~ s/\n//g;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
414 $x[$i] =~ s/\"//g;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
415 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
416 if (exists ($motif_type{$x[1]})) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
417 $motif_type{$x[1]} = $motif_type{$x[1]}." & ".$x[2];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
418 } else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
419 $motif_type{$x[1]} = $x[2];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
420 $motif_count{$x[1]} = 0;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
421 push (@motif_sequence, $x[1]);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
422 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
423 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
424 close (IN2);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
425
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
426
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
427 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
428 # 6.28.2011
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
429 # Read PhosphoSite data:
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
430 # 1) make a "kinases_PhosphoSite" array
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
431 # 2) annotate the phospho-substrates with the appropriate kinase
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
432 #
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
433 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
434
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
435
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
436 my (@kinases_PhosphoSite, $kinases_PhosphoSite);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
437 my ($p_sequence_kinase_PhosphoSite, $p_sequence_PhosphoSite, $kinase_PhosphoSite);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
438
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
439 my $line = 0;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
440
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
441 open (IN3, "$PhosphoSite_in") or die "I couldn't find $PhosphoSite_in\n";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
442 print "Reading the PhosphoSite data: $PhosphoSite_in\n";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
443
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
444 while (<IN3>) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
445 chomp;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
446 my (@x) = split(/\t/);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
447 for my $i (0 .. $#x) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
448 $x[$i] =~ s/\r//g; $x[$i] =~ s/\n//g; $x[$i] =~ s/\"//g;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
449 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
450 if ($line != 0) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
451 if (exists ($kinases_PhosphoSite -> {$x[0]})) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
452 #do nothing
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
453 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
454 else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
455 $kinases_PhosphoSite -> {$x[0]} = $x[0];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
456 push (@kinases_PhosphoSite, $x[0]);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
457 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
458 my $offset = 0;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
459 # Replace the superfluous lower case s, t and y
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
460 my @lowercase = ('s','t','y');
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
461 my @uppercase = ('S','T','Y');
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
462 for my $k (0 .. 2) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
463 my $site = 0;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
464 while ($site != -1) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
465 $site = index($x[11],$lowercase[$k], $offset);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
466 if (($site != 7) && ($site != -1)) {substr($x[11], $site, 1, $uppercase[$k]);}
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
467 $offset = $site + 1;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
468 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
469 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
470 my $tmp = $x[11]."_".$x[0]; #eg, RTPGRPLsSYGMDSR_PAK2
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
471 if (exists($p_sequence_kinase_PhosphoSite -> {$tmp})) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
472 #do nothing
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
473 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
474 else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
475 $p_sequence_kinase_PhosphoSite -> {$tmp} = $tmp;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
476 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
477 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
478 $line++;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
479 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
480 close IN3;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
481
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
482
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
483 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
484 # Read PhosphoSite regulatory site data:
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
485 # 1) make a "regulatory_sites_PhosphoSite" hash
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
486 #
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
487 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
488
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
489
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
490 my (%regulatory_sites_PhosphoSite);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
491 my (%domain, %ON_FUNCTION, %ON_PROCESS, %ON_PROT_INTERACT, %ON_OTHER_INTERACT, %notes);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
492
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
493 my $line = 0;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
494
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
495 open (IN4, "$PhosphoSite_molecular_function") or die "I couldn't find $PhosphoSite_molecular_function\n";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
496 print "Reading the PhosphoSite regulatory site data: $PhosphoSite_molecular_function\n";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
497
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
498 while (<IN4>) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
499 chomp;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
500 my (@x) = split(/\t/);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
501 for my $i (0 .. $#x) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
502 $x[$i] =~ s/\r//g; $x[$i] =~ s/\n//g; $x[$i] =~ s/\"//g;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
503 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
504 if ($line != 0) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
505 if (!exists($regulatory_sites_PhosphoSite{$x[9]})) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
506 $regulatory_sites_PhosphoSite{$x[9]} = $x[9];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
507 $domain{$x[9]} = $x[10];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
508 $ON_FUNCTION{$x[9]} = $x[11];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
509 $ON_PROCESS{$x[9]} = $x[12];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
510 $ON_PROT_INTERACT{$x[9]} = $x[13];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
511 $ON_OTHER_INTERACT{$x[9]} = $x[14];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
512 $notes{$x[9]} = $x[19];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
513 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
514 else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
515 # $domain
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
516 if ($domain{$x[9]} eq "") {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
517 $domain{$x[9]} = $domain{$x[10]};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
518 } elsif ($x[10] eq "") {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
519 # do nothing
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
520 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
521 else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
522 $domain{$x[9]} = $domain{$x[9]}." / ".$x[10];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
523 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
524
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
525 # $ON_FUNCTION
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
526 if ($ON_FUNCTION{$x[9]} eq "") {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
527 $ON_FUNCTION{$x[9]} = $ON_FUNCTION{$x[10]};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
528 } elsif ($x[10] eq "") {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
529 # do nothing
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
530 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
531 else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
532 $ON_FUNCTION{$x[9]} = $ON_FUNCTION{$x[9]}." / ".$x[10];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
533 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
534
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
535 # $ON_PROCESS
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
536 if ($ON_PROCESS{$x[9]} eq "") {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
537 $ON_PROCESS{$x[9]} = $ON_PROCESS{$x[10]};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
538 } elsif ($x[10] eq "") {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
539 # do nothing
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
540 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
541 else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
542 $ON_PROCESS{$x[9]} = $ON_PROCESS{$x[9]}." / ".$x[10];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
543 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
544
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
545 # $ON_PROT_INTERACT
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
546 if ($ON_PROT_INTERACT{$x[9]} eq "") {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
547 $ON_PROT_INTERACT{$x[9]} = $ON_PROT_INTERACT{$x[10]};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
548 } elsif ($x[10] eq "") {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
549 # do nothing
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
550 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
551 else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
552 $ON_PROT_INTERACT{$x[9]} = $ON_PROT_INTERACT{$x[9]}." / ".$x[10];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
553 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
554
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
555 # $ON_OTHER_INTERACT
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
556 if ($ON_OTHER_INTERACT{$x[9]} eq "") {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
557 $ON_OTHER_INTERACT{$x[9]} = $ON_OTHER_INTERACT{$x[10]};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
558 } elsif ($x[10] eq "") {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
559 # do nothing
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
560 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
561 else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
562 $ON_OTHER_INTERACT{$x[9]} = $ON_OTHER_INTERACT{$x[9]}." / ".$x[10];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
563 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
564
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
565 # $notes
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
566 if ($notes{$x[9]} eq "") {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
567 $notes{$x[9]} = $notes{$x[10]};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
568 } elsif ($x[10] eq "") {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
569 # do nothing
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
570 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
571 else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
572 $notes{$x[9]} = $notes{$x[9]}." / ".$x[10];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
573 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
574
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
575 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
576 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
577 $line++;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
578 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
579 close IN4;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
580
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
581 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
582 #
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
583 # Read the data file:
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
584 # 1) find sequences that match the NetworKIN predictions
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
585 # 2) find motifs that match the observed sequences
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
586 #
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
587 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
588
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
589 my ($formatted_sequence, %unique_motifs);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
590 my ($kinase_substrate_NetworKIN_matches, $kinase_motif_matches, $kinase_substrate_PhosphoSite_matches);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
591 my (%domain_2, %ON_FUNCTION_2, %ON_PROCESS_2, %ON_PROT_INTERACT_2, %N_PROT_INTERACT, %ON_OTHER_INTERACT_2, %notes_2);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
592
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
593 foreach my $peptide (keys %data) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
594 # find the unique phospho-motifs for this $peptide
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
595 my @all_motifs = ();
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
596 for my $i (0 .. $#{ $matched_sequences{$peptide} } ) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
597 my $tmp_motif = $p_motifs{$peptide}[$i];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
598 push(@all_motifs, $tmp_motif);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
599 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
600 for my $j (0 .. $#all_motifs) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
601 $all_motifs[$j] =~ s/\d+-\[\s//; $all_motifs[$j] =~ s/\s\]\-\d+//;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
602 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
603
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
604 my %seen = ();
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
605 foreach my $a (@all_motifs) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
606 if (exists($seen{$a})) { next; } else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
607 push(@{$unique_motifs{$peptide}}, $a);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
608 $seen{$a} = 1;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
609 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
610 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
611
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
612 # count the number of phospo-sites in the motif
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
613 my $number_pY = 0;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
614 my $number_pSTY = 0;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
615 if ($phospho_type eq 'y') {while (${$unique_motifs{$peptide}}[0] =~ /pY/g) {$number_pY++;}}
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
616 if ($phospho_type eq 'sty') {while (${$unique_motifs{$peptide}}[0] =~ /(pS|pT|pY)/g) {$number_pSTY++;}}
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
617
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
618 # search each of the unique motifs for matches
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
619 for my $i (0 .. $#{$unique_motifs{$peptide}}) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
620 my $tmp_motif = ${$unique_motifs{$peptide}}[$i];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
621 if (($number_pY == 1) || ($number_pSTY == 1)) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
622 my $seq_plus5aa = 0;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
623 my $seq_plus7aa = 0;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
624 $formatted_sequence = &replace_pSpTpY($tmp_motif, $phospho_type);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
625 if ($phospho_type eq 'y') {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
626 $seq_plus5aa = (split(/(\w{0,5}y\w{0,5})/, $formatted_sequence))[1];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
627 $seq_plus7aa = (split(/(\w{0,7}y\w{0,7})/, $formatted_sequence))[1];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
628 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
629 elsif ($phospho_type eq "sty") {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
630 $seq_plus5aa = (split(/(\w{0,5}(s|t|y)\w{0,5})/, $formatted_sequence))[1];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
631 $seq_plus7aa = (split(/(\w{0,7}(s|t|y)\w{0,7})/, $formatted_sequence))[1];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
632 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
633 for my $i (0 .. $#kinases_observed) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
634 my $tmp = $seq_plus5aa."_".$kinases_observed[$i]; #eg, should be PGRPLsSYGMD_PKCalpha
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
635 if (exists($p_sequence_kinase -> {$tmp})) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
636 $kinase_substrate_NetworKIN_matches{$peptide}{$kinases_observed[$i]} = "X";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
637 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
638 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
639 for my $i (0 .. $#motif_sequence) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
640 if ($peptide =~ /$motif_sequence[$i]/) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
641 $kinase_motif_matches{$peptide}{$motif_sequence[$i]} = "X";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
642 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
643 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
644 for my $i (0 .. $#kinases_PhosphoSite) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
645 my $tmp = $seq_plus7aa."_".$kinases_PhosphoSite[$i]; #eg, should be RTPGRPLsSYGMDSR_PAK2
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
646 if (exists($p_sequence_kinase_PhosphoSite -> {$tmp})) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
647 $kinase_substrate_PhosphoSite_matches{$peptide}{$kinases_PhosphoSite[$i]} = "X";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
648 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
649 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
650 if (exists($regulatory_sites_PhosphoSite{$seq_plus7aa})) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
651 $domain_2{$peptide} = $domain{$seq_plus7aa};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
652 $ON_FUNCTION_2{$peptide} = $ON_FUNCTION{$seq_plus7aa};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
653 $ON_PROCESS_2{$peptide} = $ON_PROCESS{$seq_plus7aa};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
654 $ON_PROT_INTERACT_2{$peptide} = $ON_PROT_INTERACT{$seq_plus7aa};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
655 $ON_OTHER_INTERACT_2{$peptide} = $ON_OTHER_INTERACT{$seq_plus7aa};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
656 $notes_2{$peptide} = $notes{$seq_plus7aa};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
657 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
658 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
659 elsif (($number_pY > 1) || ($number_pSTY > 1)) { #eg, if $x[4] is 1308-[ VIYFQAIEEVpYpYDHLRSAAKKR ]-1329 and $number_pY == 2
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
660 $formatted_sequence = $tmp_motif;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
661 #Create the sequences with only one phosphorylation site
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
662 #eg, 1308-[ VIYFQAIEEVpYpYDHLRSAAKKR ]-1329, which becomes 1308-[ VIYFQAIEEVpYYDHLRSAAKKR ]-1329 and 1308-[ VIYFQAIEEVYpYDHLRSAAKKR ]-1329
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
663
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
664 my (@sites, $offset, $next_p_site);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
665 $sites[0] = index($tmp_motif, "p");
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
666 $offset = $sites[0] + 1;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
667 while ($next_p_site != -1) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
668 $next_p_site = index($tmp_motif, "p", $offset);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
669 if ($next_p_site != -1) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
670 push (@sites, $next_p_site);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
671 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
672 $offset = $next_p_site+1;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
673 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
674
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
675 my @pSTY_sequences;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
676 for my $n (0 .. $#sites) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
677 $pSTY_sequences[$n] = $tmp_motif;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
678 for (my $m = $#sites; $m >= 0; $m--) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
679 if ($m != $n) {substr($pSTY_sequences[$n], $sites[$m], 1) = "";}
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
680 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
681 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
682
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
683 my @formatted_sequences;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
684 for my $k (0 .. $#sites) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
685 $formatted_sequences[$k] = &replace_pSpTpY($pSTY_sequences[$k], $phospho_type);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
686 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
687
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
688 for my $k (0 .. $#formatted_sequences) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
689 if ($phospho_type eq 'y') {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
690 $seq_plus5aa = (split(/(\w{0,5}y\w{0,5})/, $formatted_sequence[$k]))[1];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
691 $seq_plus7aa = (split(/(\w{0,7}y\w{0,7})/, $formatted_sequence[$k]))[1];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
692 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
693 elsif ($phospho_type eq "sty") {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
694 $seq_plus5aa = (split(/(\w{0,5}(s|t|y)\w{0,5})/, $formatted_sequence[$k]))[1];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
695 $seq_plus7aa = (split(/(\w{0,7}(s|t|y)\w{0,7})/, $formatted_sequence[$k]))[1];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
696 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
697 for my $i (0 .. $#kinases_observed) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
698 my $tmp = $seq_plus5aa."_".$kinases_observed[$i]; #eg, should look like REEILsEMKKV_PKCalpha
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
699 if (exists($p_sequence_kinase -> {$tmp})) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
700 $kinase_substrate_NetworKIN_matches{$peptide}{$kinases_observed[$i]} = "X";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
701 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
702 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
703 for my $i (0 .. $#motif_sequence) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
704 if ($pSTY_sequence =~ /$motif_sequence[$i]/) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
705 $kinase_motif_matches{$peptide}{$motif_sequence[$i]} = "X";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
706 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
707 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
708 for my $i (0 .. $#kinases_PhosphoSite) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
709 my $tmp = $seq_plus7aa."_".$kinases_PhosphoSite[$i]; #eg, should be RTPGRPLsSYGMDSR_PAK2
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
710 if (exists($p_sequence_kinase_PhosphoSite -> {$tmp})) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
711 $kinase_substrate_PhosphoSite_matches{$peptide}{$kinases_PhosphoSite[$i]} = "X";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
712 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
713 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
714 if (exists($regulatory_sites_PhosphoSite -> {$seq_plus7aa})) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
715 # $domain
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
716 if ($domain_2{$peptide} eq "") {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
717 $domain_2{$peptide} = $domain{$seq_plus7aa};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
718 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
719 elsif ($domain{$seq_plus7aa} eq "") {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
720 # do nothing
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
721 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
722 else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
723 $domain_2{$peptide} = $domain_2{$peptide}." / ".$domain{$seq_plus7aa};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
724 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
725
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
726 # $ON_FUNCTION_2
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
727 if ($ON_FUNCTION_2{$peptide} eq "") {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
728 $ON_FUNCTION_2{$peptide} = $ON_FUNCTION{$seq_plus7aa};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
729 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
730 elsif ($ON_FUNCTION{$seq_plus7aa} eq "") {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
731 # do nothing
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
732 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
733 else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
734 $ON_FUNCTION_2{$peptide} = $ON_FUNCTION_2{$peptide}." / ".$ON_FUNCTION{$seq_plus7aa};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
735 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
736
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
737 # $ON_PROCESS_2
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
738 if ($ON_PROCESS_2{$peptide} eq "") {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
739 $ON_PROCESS_2{$peptide} = $ON_PROCESS{$seq_plus7aa};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
740 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
741 elsif ($ON_PROCESS{$seq_plus7aa} eq "") {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
742 # do nothing
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
743 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
744 else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
745 $ON_PROCESS_2{$peptide} = $ON_PROCESS_2{$peptide}." / ".$ON_PROCESS{$seq_plus7aa};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
746 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
747
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
748 # $ON_PROT_INTERACT_2
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
749 if ($ON_PROT_INTERACT_2{$peptide} eq "") {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
750 $ON_PROT_INTERACT_2{$peptide} = $ON_PROT_INTERACT{$seq_plus7aa};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
751 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
752 elsif ($ON_PROT_INTERACT{$seq_plus7aa} eq "") {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
753 # do nothing
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
754 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
755 else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
756 $ON_PROT_INTERACT_2{$peptide} = $ON_PROT_INTERACT_2{$peptide}." / ".$ON_PROT_INTERACT{$seq_plus7aa};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
757 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
758
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
759 # $ON_OTHER_INTERACT_2
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
760 if ($ON_OTHER_INTERACT_2{$peptide} eq "") {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
761 $ON_OTHER_INTERACT_2{$peptide} = $ON_OTHER_INTERACT{$seq_plus7aa};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
762 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
763 elsif ($ON_OTHER_INTERACT{$seq_plus7aa} eq "") {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
764 # do nothing
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
765 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
766 else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
767 $ON_OTHER_INTERACT_2{$peptide} = $ON_OTHER_INTERACT_2{$peptide}." / ".$ON_OTHER_INTERACT{$seq_plus7aa};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
768 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
769
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
770 # $notes_2
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
771 if ($notes_2{$peptide} eq "") {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
772 $notes_2{$peptide} = $notes{$seq_plus7aa};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
773 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
774 elsif ($notes{$seq_plus7aa} eq "") {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
775 # do nothing
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
776 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
777 else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
778 $notes_2{$peptide} = $notes_2{$peptide}." / ".$notes{$seq_plus7aa};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
779 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
780 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
781 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
782 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
783 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
784 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
785
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
786
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
787 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
788 #
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
789 # Print to the output file
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
790 #
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
791 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
792 open (OUT, ">$file_out") || die "could not open the fileout: $file_out";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
793
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
794 # print the header info
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
795 print OUT "p-peptide\tProtein description\tGene name(s)\tFASTA name\tPhospho-sites\tUnique phospho-motifs, no residue numbers\tAccessions\tPhospho-motifs for all members of protein group with residue numbers\t";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
796
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
797 # print the PhosphoSite regulatory data
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
798 print OUT "Domain\tON_FUNCTION\tON_PROCESS\tON_PROT_INTERACT\tON_OTHER_INTERACT\tPhosphoSite notes\t";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
799
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
800 # print the sample names
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
801 for my $i (0 .. $#samples) { print OUT "$samples[$i]\t"; }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
802
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
803 # print the kinases and groups
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
804 for my $i (0 .. $#kinases_observed) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
805 my $temp = $kinases_observed[$i]."_NetworKIN";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
806 print OUT "$temp\t";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
807 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
808 for my $i (0 .. $#motif_sequence) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
809 print OUT "$motif_type{$motif_sequence[$i]} ($motif_sequence[$i])\t";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
810 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
811 for my $i (0 .. $#kinases_PhosphoSite) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
812 my $temp = $kinases_PhosphoSite[$i]."_PhosphoSite";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
813 if ($i < $#kinases_PhosphoSite) { print OUT "$temp\t"; }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
814 if ($i == $#kinases_PhosphoSite) { print OUT "$temp\n"; }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
815 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
816
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
817
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
818 foreach my $peptide (keys %data) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
819 # Print the peptide itself
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
820 print OUT "$peptide\t";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
821
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
822 # skip over failed matches
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
823 if ($matched_sequences{$peptide} eq "Failed match") {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
824 print OUT "Sequence not found in FASTA database\tNA\tNA\tNA\tNA\tNA\tNA\t";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
825 } else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
826 # Print just the protein description
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
827 my @description = ();
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
828 for $i (0 .. $#{$names{$peptide}}) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
829 my $long_name = $names{$peptide}[$i];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
830 my @naming_parts = split(/\sOS/, $long_name);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
831 my @front_half = split(/\s/, $naming_parts[0]);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
832 push(@description, join(" ", @front_half[1..($#front_half)]));
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
833 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
834 print OUT join(" /// ", @description), "\t";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
835
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
836 # Print just the gene name
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
837 my @gene = ();
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
838 my %seen = ();
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
839 for $i (0 .. $#{$names{$peptide}}) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
840 my $tmp_gene = $names{$peptide}[$i];
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
841 $tmp_gene =~ s/^.*GN=//;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
842 $tmp_gene =~ s/\s.*//;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
843 if (!exists($seen{$tmp_gene})) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
844 push(@gene, $tmp_gene);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
845 $seen{$tmp_gene} = $tmp_gene;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
846 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
847 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
848 print OUT join(" /// ", @gene), "\t";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
849
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
850 # print the entire names
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
851 print OUT join(" /// ", @{$names{$peptide}}), "\t";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
852
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
853 # Print the phospho-residues
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
854 for my $i (0 .. $#{ $matched_sequences{$peptide} } ) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
855 if ($i < $#{ $matched_sequences{$peptide} }) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
856 @tmp_p_residues = @{$p_residues{$peptide}{$i}};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
857 for my $j (0 .. $#tmp_p_residues) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
858 if ($j < $#tmp_p_residues) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
859 my $tmp_site_for_printing = $p_residues{$peptide}{$i}[$j] + 1; # added 12.05.2012 for Justin's data
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
860 print OUT "p$residues{$peptide}{$i}[$j]$tmp_site_for_printing, ";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
861 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
862 elsif ($j == $#tmp_p_residues) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
863 my $tmp_site_for_printing = $p_residues{$peptide}{$i}[$j] + 1; # added 12.05.2012 for Justin's data
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
864 print OUT "p$residues{$peptide}{$i}[$j]$tmp_site_for_printing /// ";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
865 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
866 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
867 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
868 elsif ($i == $#{ $matched_sequences{$peptide} }) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
869 @tmp_p_residues = @{$p_residues{$peptide}{$i}};
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
870 for my $j (0 .. $#tmp_p_residues) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
871 if ($j < $#tmp_p_residues) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
872 my $tmp_site_for_printing = $p_residues{$peptide}{$i}[$j] + 1; # added 12.05.2012 for Justin's data
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
873 print OUT "p$residues{$peptide}{$i}[$j]$tmp_site_for_printing, ";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
874 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
875 elsif ($j == $#tmp_p_residues) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
876 my $tmp_site_for_printing = $p_residues{$peptide}{$i}[$j] + 1; # added 12.05.2012 for Justin's data
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
877 print OUT "p$residues{$peptide}{$i}[$j]$tmp_site_for_printing\t";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
878 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
879 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
880 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
881 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
882
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
883 # Print the UNIQUE phospho-motifs
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
884 print OUT join(" /// ", @{$unique_motifs{$peptide}}), "\t";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
885
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
886 # Print the accessions
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
887 print OUT join(" /// ", @{$accessions{$peptide}}), "\t";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
888
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
889 # print ALL motifs with residue numbers
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
890 print OUT join(" /// ", @{$p_motifs{$peptide}}), "\t";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
891 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
892
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
893 # Print the PhosphoSite regulatory data
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
894
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
895 if (exists($domain_2{$peptide})) { print OUT "$domain_2{$peptide}\t"; } else { print OUT "\t"; }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
896 if (exists($ON_FUNCTION_2{$peptide})) { print OUT "$ON_FUNCTION_2{$peptide}\t"; } else { print OUT "\t"; }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
897 if (exists($ON_PROCESS_2{$peptide})) { print OUT "$ON_PROCESS_2{$peptide}\t"; } else { print OUT "\t"; }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
898 if (exists($ON_PROT_INTERACT_2{$peptide})) { print OUT "$ON_PROT_INTERACT_2{$peptide}\t"; } else { print OUT "\t"; }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
899 if (exists($ON_OTHER_INTERACT_2{$peptide})) { print OUT "$ON_OTHER_INTERACT_2{$peptide}\t"; } else { print OUT "\t"; }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
900 if (exists($notes_2{$peptide})) { print OUT "$notes_2{$peptide}\t"; } else { print OUT "\t"; }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
901
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
902 # Print the data
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
903 @tmp_data = (); foreach (@{$data{$peptide}}) { push(@tmp_data, $_); }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
904 print OUT join("\t", @tmp_data), "\t";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
905
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
906 # print the kinase-substrate data
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
907 for my $i (0 .. $#kinases_observed) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
908 if (exists($kinase_substrate_NetworKIN_matches{$peptide}{$kinases_observed[$i]})) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
909 print OUT "X\t";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
910 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
911 else { print OUT "\t";}
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
912 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
913 for my $i (0 .. $#motif_sequence) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
914 if (exists($kinase_motif_matches{$peptide}{$motif_sequence[$i]})) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
915 print OUT "X\t";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
916 # print "Line 657: i is $i\t$kinase_motif_matches{$peptide}{$motif_sequence[$i]}\n"; #debug
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
917 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
918 else { print OUT "\t";}
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
919 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
920 for my $i (0 .. $#kinases_PhosphoSite) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
921 if (exists($kinase_substrate_PhosphoSite_matches{$peptide}{$kinases_PhosphoSite[$i]}) && ($i < $#kinases_PhosphoSite)) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
922 print OUT "X\t";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
923 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
924 elsif (exists($kinase_substrate_PhosphoSite_matches{$peptide}{$kinases_PhosphoSite[$i]}) && ($i == $#kinases_PhosphoSite)) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
925 print OUT "X\n";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
926 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
927 elsif (!exists($kinase_substrate_PhosphoSite_matches{$peptide}{$kinases_PhosphoSite[$i]}) && ($i < $#kinases_PhosphoSite)) {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
928 print OUT "\t";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
929 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
930 else {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
931 print OUT "\n";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
932 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
933 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
934 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
935
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
936 close OUT;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
937
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
938
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
939 my @timeData = localtime(time);
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
940 print "\nFinished $timeData[2]:$timeData[1]:$timeData[0]\n\n";
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
941
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
942 ###############################################################################################################################
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
943 sub replace_pSpTpY {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
944 my ($formatted_sequence, $phospho_type) = @_;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
945 if ($phospho_type eq 'y') {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
946 $formatted_sequence =~ s/pS/S/g;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
947 $formatted_sequence =~ s/pT/T/g;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
948 $formatted_sequence =~ s/pY/y/g;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
949 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
950 elsif ($phospho_type eq "sty") {
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
951 $formatted_sequence =~ s/pS/s/g;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
952 $formatted_sequence =~ s/pT/t/g;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
953 $formatted_sequence =~ s/pY/y/g;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
954 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
955 $formatted_sequence;
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
956 }
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
galaxyp
parents:
diff changeset
957