Mercurial > repos > drosofff > msp_sr_signature
annotate signature.py @ 11:b1a15b5a3f1b draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
| author | drosofff |
|---|---|
| date | Wed, 07 Jun 2017 17:54:01 -0400 |
| parents | 2b30861d95f4 |
| children |
| rev | line source |
|---|---|
| 0 | 1 #!/usr/bin/python |
| 2 # script for computing overlap signatures from a bowtie output | |
| 3 # Christophe Antoniewski <drosofff@gmail.com> | |
| 4 # Usage signature.py <1:input> <2:format of input> <3:minsize query> <4:maxsize query> <5:minsize target> <6:maxsize target> | |
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b1a15b5a3f1b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
drosofff
parents:
2
diff
changeset
|
5 # <7:minscope> <8:maxscope> <9:output> <10:bowtie index> <11:procedure option> <12: graph (global or lattice)> |
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b1a15b5a3f1b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
drosofff
parents:
2
diff
changeset
|
6 # <13: R code> |
| 0 | 7 # version 2.0.0 |
| 8 | |
| 2 | 9 import subprocess |
| 10 import argparse | |
|
11
b1a15b5a3f1b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
drosofff
parents:
2
diff
changeset
|
11 from smRtools import HandleSmRNAwindows |
| 2 | 12 |
| 0 | 13 |
| 14 def Parser(): | |
| 2 | 15 the_parser = argparse.ArgumentParser() |
| 16 the_parser.add_argument( | |
| 17 '--input', action="store", type=str, help="input alignment file") | |
| 18 the_parser.add_argument('--inputFormat', action="store", type=str, choices=[ | |
| 19 "tabular", "bam", "sam"], help="format of alignment file (tabular/bam/sam)") | |
| 20 the_parser.add_argument( | |
| 21 '--minquery', type=int, help="Minimum readsize of query reads (nt) - must be an integer") | |
| 22 the_parser.add_argument( | |
| 23 '--maxquery', type=int, help="Maximum readsize of query reads (nt) - must be an integer") | |
| 24 the_parser.add_argument( | |
| 25 '--mintarget', type=int, help="Minimum readsize of target reads (nt) - must be an integer") | |
| 26 the_parser.add_argument( | |
| 27 '--maxtarget', type=int, help="Maximum readsize of target reads (nt) - must be an integer") | |
| 28 the_parser.add_argument( | |
| 29 '--minscope', type=int, help="Minimum overlap analyzed (nt) - must be an integer") | |
| 30 the_parser.add_argument( | |
| 31 '--maxscope', type=int, help="Maximum overlap analyzed (nt) - must be an integer") | |
| 32 the_parser.add_argument( | |
| 33 '--outputOverlapDataframe', action="store", type=str, help="Overlap dataframe") | |
| 34 the_parser.add_argument('--referenceGenome', action='store', | |
| 35 help="path to the bowtie-indexed or fasta reference") | |
| 36 the_parser.add_argument('--extract_index', action='store_true', | |
| 37 help="specify if the reference is an indexed Bowtie reference") | |
| 38 the_parser.add_argument('--graph', action='store', choices=[ | |
| 39 "global", "lattice"], help="small RNA signature is computed either globally or by item (global-lattice)") | |
| 40 the_parser.add_argument( | |
| 41 '--rcode', type=str, help="R code to be passed to the python script") | |
| 42 args = the_parser.parse_args() | |
| 43 return args | |
| 0 | 44 |
| 45 args = Parser() | |
| 46 | |
| 47 if args.extract_index: | |
| 2 | 48 GenomeFormat = "bowtieIndex" |
| 0 | 49 else: |
| 2 | 50 GenomeFormat = "fastaSource" |
| 0 | 51 |
| 52 if args.inputFormat == "tabular": | |
| 2 | 53 Genome = HandleSmRNAwindows( |
| 54 args.input, args.inputFormat, args.referenceGenome, GenomeFormat) | |
| 0 | 55 elif args.inputFormat == "sam": |
| 2 | 56 Genome = HandleSmRNAwindows( |
| 57 args.input, args.inputFormat, args.referenceGenome, GenomeFormat) | |
| 0 | 58 else: |
| 2 | 59 Genome = HandleSmRNAwindows( |
| 60 args.input, args.inputFormat, args.referenceGenome, GenomeFormat) | |
| 0 | 61 |
| 62 # replace objDic by Genome.instanceDict or... objDic = Genome.instanceDict | |
| 63 objDic = Genome.instanceDict | |
| 64 | |
| 65 args.maxscope += 1 | |
| 66 | |
| 2 | 67 general_frequency_table = dict( |
| 68 [(i, 0) for i in range(args.minscope, args.maxscope)]) | |
| 69 general_percent_table = dict( | |
| 70 [(i, 0) for i in range(args.minscope, args.maxscope)]) | |
| 71 OUT = open(args.outputOverlapDataframe, "w") | |
| 0 | 72 |
| 73 if args.graph == "global": | |
| 2 | 74 # for normalized summing of local_percent_table(s) |
| 75 readcount_dic = {} | |
| 76 Total_read_in_objDic = 0 | |
| 77 for item in objDic: | |
| 78 readcount_dic[item] = objDic[item].readcount( | |
| 79 args.minquery, args.maxquery) | |
| 80 Total_read_in_objDic += readcount_dic[item] | |
| 81 ###### | |
| 82 for x in (objDic): | |
| 83 local_frequency_table = objDic[x].signature( | |
| 84 args.minquery, args.maxquery, args.mintarget, args.maxtarget, range(args.minscope, args.maxscope)) | |
| 85 local_percent_table = objDic[x].hannon_signature( | |
| 86 args.minquery, args.maxquery, args.mintarget, args.maxtarget, range(args.minscope, args.maxscope)) | |
| 87 try: | |
| 88 for overlap in local_frequency_table.keys(): | |
| 89 general_frequency_table[overlap] = general_frequency_table.get( | |
| 90 overlap, 0) + local_frequency_table[overlap] | |
| 91 except: | |
| 92 pass | |
| 93 try: | |
| 94 for overlap in local_percent_table.keys(): | |
| 95 general_percent_table[overlap] = general_percent_table.get( | |
| 96 overlap, 0) + (1. / Total_read_in_objDic * readcount_dic[x] * local_percent_table[overlap]) | |
| 97 except: | |
| 98 pass | |
| 99 print >> OUT, "overlap\tnum of pairs\tprobability" | |
| 100 for classe in sorted(general_frequency_table): | |
| 101 print >> OUT, "%i\t%i\t%f" % ( | |
| 102 classe, general_frequency_table[classe], general_percent_table[classe]) | |
| 0 | 103 |
| 104 else: | |
| 2 | 105 print >> OUT, "overlap\tnum of pairs\tprobability\titem" |
| 106 for x in (objDic): | |
| 107 local_frequency_table = objDic[x].signature( | |
| 108 args.minquery, args.maxquery, args.mintarget, args.maxtarget, range(args.minscope, args.maxscope)) | |
| 109 local_percent_table = objDic[x].hannon_signature( | |
| 110 args.minquery, args.maxquery, args.mintarget, args.maxtarget, range(args.minscope, args.maxscope)) | |
| 111 for classe in range(args.minscope, args.maxscope): | |
| 112 print >> OUT, "%i\t%i\t%f\t%s" % ( | |
| 113 classe, local_frequency_table[classe], local_percent_table[classe], x) | |
| 0 | 114 |
| 115 OUT.close() | |
| 116 | |
| 2 | 117 # Run the R script that is defined in the xml using the Rscript binary |
| 118 # provided with R. | |
| 119 R_command = "Rscript " + args.rcode | |
| 0 | 120 process = subprocess.Popen(R_command.split()) |