Mercurial > repos > galaxyp > retrieve_ensembl_bed

annotate bedutil.py @ 0:887e111c0919 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
author galaxyp
date Sun, 14 Jan 2018 14:11:53 -0500
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children c3d600729b6f
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0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
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1 #!/usr/bin/env python
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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2 """
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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3 #
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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4 #------------------------------------------------------------------------------
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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5 # University of Minnesota
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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6 # Copyright 2016, Regents of the University of Minnesota
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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7 #------------------------------------------------------------------------------
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8 # Author:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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9 #
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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10 # James E Johnson
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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11 #
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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12 #------------------------------------------------------------------------------
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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13 """
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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14
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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15 import sys
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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16
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17 from Bio.Seq import reverse_complement, translate
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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19
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20 def bed_from_line(line, ensembl=False, seq_column=None):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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21 fields = line.rstrip('\r\n').split('\t')
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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22 if len(fields) < 12:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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23 return None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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24 (chrom, chromStart, chromEnd, name, score, strand,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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25 thickStart, thickEnd, itemRgb,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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26 blockCount, blockSizes, blockStarts) = fields[0:12]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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27 bed_entry = BedEntry(chrom=chrom, chromStart=chromStart, chromEnd=chromEnd,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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28 name=name, score=score, strand=strand,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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29 thickStart=thickStart, thickEnd=thickEnd,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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30 itemRgb=itemRgb,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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31 blockCount=blockCount,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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32 blockSizes=blockSizes.rstrip(','),
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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33 blockStarts=blockStarts.rstrip(','))
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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34 if seq_column is not None and -len(fields) <= seq_column < len(fields):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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35 bed_entry.seq = fields[seq_column]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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36 if ensembl and len(fields) >= 20:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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37 bed_entry.second_name = fields[12]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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38 bed_entry.cds_start_status = fields[13]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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39 bed_entry.cds_end_status = fields[14]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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40 bed_entry.exon_frames = fields[15].rstrip(',')
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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41 bed_entry.biotype = fields[16]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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42 bed_entry.gene_name = fields[17]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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43 bed_entry.second_gene_name = fields[18]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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44 bed_entry.gene_type = fields[19]
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45 return bed_entry
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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46
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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47
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48 class BedEntry(object):
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49 def __init__(self, chrom=None, chromStart=None, chromEnd=None,
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50 name=None, score=None, strand=None,
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51 thickStart=None, thickEnd=None, itemRgb=None,
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52 blockCount=None, blockSizes=None, blockStarts=None):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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53 self.chrom = chrom
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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54 self.chromStart = int(chromStart)
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55 self.chromEnd = int(chromEnd)
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56 self.name = name
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57 self.score = int(score) if score is not None else 0
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58 self.strand = '-' if str(strand).startswith('-') else '+'
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59 self.thickStart = int(thickStart) if thickStart else self.chromStart
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60 self.thickEnd = int(thickEnd) if thickEnd else self.chromEnd
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61 self.itemRgb = str(itemRgb) if itemRgb is not None else r'100,100,100'
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62 self.blockCount = int(blockCount)
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63 if isinstance(blockSizes, str) or isinstance(blockSizes, unicode):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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64 self.blockSizes = [int(x) for x in blockSizes.split(',')]
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65 elif isinstance(blockSizes, list):
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66 self.blockSizes = [int(x) for x in blockSizes]
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67 else:
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68 self.blockSizes = blockSizes
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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69 if isinstance(blockStarts, str) or isinstance(blockSizes, unicode):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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70 self.blockStarts = [int(x) for x in blockStarts.split(',')]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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71 elif isinstance(blockStarts, list):
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72 self.blockStarts = [int(x) for x in blockStarts]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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73 else:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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74 self.blockStarts = blockStarts
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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75 self.second_name = None
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76 self.cds_start_status = None
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77 self.cds_end_status = None
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78 self.exon_frames = None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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diff changeset
79 self.biotype = None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
80 self.gene_name = None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
81 self.second_gene_name = None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
82 self.gene_type = None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
83 self.seq = None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
84 self.cdna = None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
85 self.pep = None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
86 # T26C
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
87 self.aa_change = []
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
88 # p.Trp26Cys g.<pos><ref>><alt> # g.1304573A>G
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
89 self.variants = []
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
90
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
91 def __str__(self):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
92 return '%s\t%d\t%d\t%s\t%d\t%s\t%d\t%d\t%s\t%d\t%s\t%s' % (
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
93 self.chrom, self.chromStart, self.chromEnd,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
94 self.name, self.score, self.strand,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
95 self.thickStart, self.thickEnd, str(self.itemRgb), self.blockCount,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
96 ','.join([str(x) for x in self.blockSizes]),
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
97 ','.join([str(x) for x in self.blockStarts]))
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
98
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
99 def get_splice_junctions(self):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
100 splice_juncs = []
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
101 for i in range(self.blockCount - 1):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
102 splice_junc = "%s:%d_%d"\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
103 % (self.chrom,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
104 self.chromStart + self.blockSizes[i],
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
105 self.chromStart + self.blockStarts[i+1])
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
106 splice_juncs.append(splice_junc)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
107 return splice_juncs
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
108
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
109 def get_exon_seqs(self):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
110 if not self.seq:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
111 return None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
112 exons = []
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
113 for i in range(self.blockCount):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
114 exons.append(self.seq[self.blockStarts[i]:self.blockStarts[i]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
115 + self.blockSizes[i]])
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
116 if self.strand == '-': # reverse complement
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
117 exons.reverse()
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
118 for i, s in enumerate(exons):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
119 exons[i] = reverse_complement(s)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
120 return exons
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
121
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
122 def get_spliced_seq(self, strand=None):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
123 if not self.seq:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
124 return None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
125 seq = ''.join(self.get_exon_seqs())
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
126 if strand and self.strand != strand:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
127 seq = reverse_complement(seq)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
128 return seq
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
129
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
130 def get_cdna(self):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
131 if not self.cdna:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
132 self.cdna = self.get_spliced_seq()
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
133 return self.cdna
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
134
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
135 def get_cds(self):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
136 cdna = self.get_cdna()
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
137 if cdna:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
138 if self.chromStart == self.thickStart\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
139 and self.chromEnd == self.thickEnd:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
140 return cdna
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
141 pos = [self.cdna_offset_of_pos(self.thickStart),
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
142 self.cdna_offset_of_pos(self.thickEnd)]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
143 if 0 <= min(pos) <= max(pos) <= len(cdna):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
144 return cdna[min(pos):max(pos)]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
145 return None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
146
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
147 def set_cds(self, cdna_start, cdna_end):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
148 cdna_len = sum(self.blockSizes)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
149 if 0 <= cdna_start < cdna_end <= cdna_len:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
150 cds_pos = [self.pos_of_cdna_offet(cdna_start),
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
151 self.pos_of_cdna_offet(cdna_end)]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
152 if all(cds_pos):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
153 self.thickStart = min(cds_pos)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
154 self.thickEnd = max(cds_pos)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
155 return self
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
156 return None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
157
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
158 def trim_cds(self, basepairs):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
159 if self.chromStart <= self.thickStart < self.thickEnd <= self.chromEnd:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
160 cds_pos = [self.cdna_offset_of_pos(self.thickStart),
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
161 self.cdna_offset_of_pos(self.thickEnd)]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
162 if basepairs > 0:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
163 return self.set_cds(min(cds_pos) + basepairs, max(cds_pos))
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
164 else:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
165 return self.set_cds(min(cds_pos), max(cds_pos) + basepairs)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
166 return None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
167
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
168 def get_cigar(self):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
169 cigar = ''
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
170 r = range(self.blockCount)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
171 xl = None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
172 for x in r:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
173 if xl is not None:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
174 intronSize = abs(self.blockStarts[x] - self.blockSizes[xl]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
175 - self.blockStarts[xl])
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
176 cigar += '%dN' % intronSize
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
177 cigar += '%dM' % self.blockSizes[x]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
178 xl = x
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
179 return cigar
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
180
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
181 def get_cigar_md(self):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
182 cigar = ''
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
183 md = ''
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
184 r = range(self.blockCount)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
185 xl = None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
186 for x in r:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
187 if xl is not None:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
188 intronSize = abs(self.blockStarts[x] - self.blockSizes[xl]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
189 - self.blockStarts[xl])
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
190 cigar += '%dN' % intronSize
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
191 cigar += '%dM' % self.blockSizes[x]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
192 xl = x
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
193 md = '%d' % sum(self.blockSizes)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
194 return (cigar, md)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
195
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
196 def get_translation(self, sequence=None):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
197 translation = None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
198 seq = sequence if sequence else self.get_spliced_seq()
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
199 if seq:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
200 seqlen = len(seq) / 3 * 3
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
201 if seqlen >= 3:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
202 translation = translate(seq[:seqlen])
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
203 return translation
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
204
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
205 def get_translations(self):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
206 translations = []
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
207 seq = self.get_spliced_seq()
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
208 if seq:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
209 for i in range(3):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
210 translation = self.get_translation(sequence=seq[i:])
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
211 if translation:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
212 translations.append(translation)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
213 return translations
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
214
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
215 def pos_of_cdna_offet(self, offset):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
216 if offset is not None and 0 <= offset < sum(self.blockSizes):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
217 r = range(self.blockCount)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
218 rev = self.strand == '-'
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
219 if rev:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
220 r.reverse()
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
221 nlen = 0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
222 for x in r:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
223 if offset < nlen + self.blockSizes[x]:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
224 if rev:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
225 return self.chromStart + self.blockStarts[x]\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
226 + self.blockSizes[x] - (offset - nlen)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
227 else:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
228 return self.chromStart + self.blockStarts[x]\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
229 + (offset - nlen)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
230 nlen += self.blockSizes[x]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
231 return None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
232
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
233 def cdna_offset_of_pos(self, pos):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
234 if not self.chromStart <= pos < self.chromEnd:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
235 return -1
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
236 r = range(self.blockCount)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
237 rev = self.strand == '-'
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
238 if rev:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
239 r.reverse()
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
240 nlen = 0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
241 for x in r:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
242 bStart = self.chromStart + self.blockStarts[x]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
243 bEnd = bStart + self.blockSizes[x]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
244 if bStart <= pos < bEnd:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
245 return nlen + (bEnd - pos if rev else pos - bStart)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
246 nlen += self.blockSizes[x]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
247
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
248 def apply_variant(self, pos, ref, alt):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
249 pos = int(pos)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
250 if not ref or not alt:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
251 print >> sys.stderr, "variant requires ref and alt sequences"
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
252 return
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
253 if not self.chromStart <= pos <= self.chromEnd:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
254 print >> sys.stderr, "variant not in entry %s: %s %d < %d < %d"\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
255 % (self.name, self.strand, self.chromStart, pos, self.chromEnd)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
256 print >> sys.stderr, "%s" % str(self)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
257 return
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
258 if len(ref) != len(alt):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
259 print >> sys.stderr, "variant only works for snp: %s %s"\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
260 % (ref, alt)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
261 return
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
262 if not self.seq:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
263 print >> sys.stderr, "variant entry %s has no seq" % self.name
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
264 return
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
265 """
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
266 if self.strand == '-':
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
267 ref = reverse_complement(ref)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
268 alt = reverse_complement(alt)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
269 """
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
270 bases = list(self.seq)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
271 offset = pos - self.chromStart
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
272 for i in range(len(ref)):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
273 # offset = self.cdna_offset_of_pos(pos+i)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
274 if offset is not None:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
275 bases[offset+i] = alt[i]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
276 else:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
277 print >> sys.stderr,\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
278 "variant offset %s: %s %d < %d < %d"\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
279 % (self.name, self.strand, self.chromStart,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
280 pos+1, self.chromEnd)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
281 print >> sys.stderr, "%s" % str(self)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
282 self.seq = ''.join(bases)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
283 self.variants.append("g.%d%s>%s" % (pos+1, ref, alt))
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
284
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
285 def get_variant_bed(self, pos, ref, alt):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
286 pos = int(pos)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
287 if not ref or not alt:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
288 print >> sys.stderr, "variant requires ref and alt sequences"
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
289 return None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
290 if not self.chromStart <= pos <= self.chromEnd:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
291 print >> sys.stderr,\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
292 "variant not in entry %s: %s %d < %d < %d"\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
293 % (self.name, self.strand, self.chromStart, pos, self.chromEnd)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
294 print >> sys.stderr, "%s" % str(self)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
295 return None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
296 if not self.seq:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
297 print >> sys.stderr, "variant entry %s has no seq" % self.name
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
298 return None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
299 tbed = BedEntry(chrom=self.chrom,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
300 chromStart=self.chromStart, chromEnd=self.chromEnd,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
301 name=self.name, score=self.score, strand=self.strand,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
302 thickStart=self.chromStart, thickEnd=self.chromEnd,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
303 itemRgb=self.itemRgb,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
304 blockCount=self.blockCount,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
305 blockSizes=self.blockSizes,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
306 blockStarts=self.blockStarts)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
307 bases = list(self.seq)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
308 offset = pos - self.chromStart
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
309 tbed.seq = ''.join(bases[:offset] + list(alt)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
310 + bases[offset+len(ref):])
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
311 if len(ref) != len(alt):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
312 diff = len(alt) - len(ref)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
313 rEnd = pos + len(ref)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
314 # need to adjust blocks
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
315 # change spans blocks,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
316 for x in range(tbed.blockCount):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
317 bStart = tbed.chromStart + tbed.blockStarts[x]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
318 bEnd = bStart + tbed.blockSizes[x]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
319 # change within a block or extends (last block)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
320 # adjust blocksize
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
321 # seq: GGGcatGGG
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
322 # ref c alt tag: GGGtagatGGG
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
323 # ref cat alt a: GGGaGGG
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
324 if bStart <= pos < rEnd < bEnd:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
325 tbed.blockSizes[x] += diff
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
326 return tbed
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
327
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
328 # (start, end)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
329 def get_subrange(self, tstart, tstop, debug=False):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
330 chromStart = self.chromStart
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
331 chromEnd = self.chromEnd
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
332 if debug:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
333 print >> sys.stderr, "%s" % (str(self))
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
334 r = range(self.blockCount)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
335 if self.strand == '-':
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
336 r.reverse()
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
337 bStart = 0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
338 bEnd = 0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
339 for x in r:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
340 bEnd = bStart + self.blockSizes[x]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
341 if bStart <= tstart < bEnd:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
342 if self.strand == '+':
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
343 chromStart = self.chromStart + self.blockStarts[x] +\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
344 (tstart - bStart)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
345 else:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
346 chromEnd = self.chromStart + self.blockStarts[x] +\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
347 self.blockSizes[x] - (tstart - bStart)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
348 if bStart <= tstop < bEnd:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
349 if self.strand == '+':
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
350 chromEnd = self.chromStart + self.blockStarts[x] +\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
351 (tstop - bStart)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
352 else:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
353 chromStart = self.chromStart + self.blockStarts[x] +\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
354 self.blockSizes[x] - (tstop - bStart)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
355 if debug:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
356 print >> sys.stderr,\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
357 "%3d %s\t%d\t%d\t%d\t%d\t%d\t%d"\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
358 % (x, self.strand, bStart, bEnd,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
359 tstart, tstop, chromStart, chromEnd)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
360 bStart += self.blockSizes[x]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
361 return(chromStart, chromEnd)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
362
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
363 # get the blocks for sub range
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
364 def get_blocks(self, chromStart, chromEnd):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
365 tblockCount = 0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
366 tblockSizes = []
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
367 tblockStarts = []
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
368 for x in range(self.blockCount):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
369 bStart = self.chromStart + self.blockStarts[x]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
370 bEnd = bStart + self.blockSizes[x]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
371 if bStart > chromEnd:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
372 break
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
373 if bEnd < chromStart:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
374 continue
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
375 cStart = max(chromStart, bStart)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
376 tblockStarts.append(cStart - chromStart)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
377 tblockSizes.append(min(chromEnd, bEnd) - cStart)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
378 tblockCount += 1
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
379 return (tblockCount, tblockSizes, tblockStarts)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
380
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
381 def trim(self, tstart, tstop, debug=False):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
382 (tchromStart, tchromEnd) =\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
383 self.get_subrange(tstart, tstop, debug=debug)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
384 (tblockCount, tblockSizes, tblockStarts) =\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
385 self.get_blocks(tchromStart, tchromEnd)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
386 tbed = BedEntry(
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
387 chrom=self.chrom, chromStart=tchromStart, chromEnd=tchromEnd,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
388 name=self.name, score=self.score, strand=self.strand,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
389 thickStart=tchromStart, thickEnd=tchromEnd, itemRgb=self.itemRgb,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
390 blockCount=tblockCount,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
391 blockSizes=tblockSizes, blockStarts=tblockStarts)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
392 if self.seq:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
393 ts = tchromStart-self.chromStart
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
394 te = tchromEnd - tchromStart + ts
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
395 tbed.seq = self.seq[ts:te]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
396 return tbed
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
397
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
398 def get_filtered_translations(self, untrimmed=False, filtering=True,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
399 ignore_left_bp=0, ignore_right_bp=0,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
400 debug=False):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
401 translations = [None, None, None]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
402 seq = self.get_spliced_seq()
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
403 ignore = (ignore_left_bp if self.strand == '+'
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
404 else ignore_right_bp) / 3
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
405 block_sum = sum(self.blockSizes)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
406 exon_sizes = [x for x in self.blockSizes]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
407 if self.strand == '-':
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
408 exon_sizes.reverse()
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
409 splice_sites = [sum(exon_sizes[:x]) / 3
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
410 for x in range(1, len(exon_sizes))]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
411 if debug:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
412 print >> sys.stderr, "splice_sites: %s" % splice_sites
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
413 junc = splice_sites[0] if len(splice_sites) > 0 else exon_sizes[0]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
414 if seq:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
415 for i in range(3):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
416 translation = self.get_translation(sequence=seq[i:])
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
417 if translation:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
418 tstart = 0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
419 tstop = len(translation)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
420 offset = (block_sum - i) % 3
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
421 if debug:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
422 print >> sys.stderr,\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
423 "frame: %d\ttstart: %d tstop: %d offset: %d\t%s"\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
424 % (i, tstart, tstop, offset, translation)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
425 if not untrimmed:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
426 tstart = translation.rfind('*', 0, junc) + 1
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
427 stop = translation.find('*', junc)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
428 tstop = stop if stop >= 0 else len(translation)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
429 offset = (block_sum - i) % 3
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
430 trimmed = translation[tstart:tstop]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
431 if debug:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
432 print >> sys.stderr,\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
433 "frame: %d\ttstart: %d tstop: %d offset: %d\t%s"\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
434 % (i, tstart, tstop, offset, trimmed)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
435 if filtering and tstart > ignore:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
436 continue
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
437 # get genomic locations for start and end
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
438 if self.strand == '+':
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
439 chromStart = self.chromStart + i + (tstart * 3)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
440 chromEnd = self.chromEnd - offset\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
441 - (len(translation) - tstop) * 3
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
442 else:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
443 chromStart = self.chromStart + offset\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
444 + (len(translation) - tstop) * 3
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
445 chromEnd = self.chromEnd - i - (tstart * 3)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
446 # get the blocks for this translation
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
447 (tblockCount, tblockSizes, tblockStarts) =\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
448 self.get_blocks(chromStart, chromEnd)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
449 translations[i] = (chromStart, chromEnd, trimmed,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
450 tblockCount, tblockSizes, tblockStarts)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
451 if debug:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
452 print >> sys.stderr,\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
453 "tblockCount: %d tblockStarts: %s tblockSizes: %s"\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
454 % (tblockCount, tblockStarts, tblockSizes)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
455 return translations
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
456
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
457 def get_seq_id(self, seqtype='unk:unk', reference='', frame=None):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
458 # Ensembl fasta ID format
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
459 # >ID SEQTYPE:STATUS LOCATION GENE TRANSCRIPT
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
460 # >ENSP00000328693 pep:splice chromosome:NCBI35:1:904515:910768:1\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
461 # gene:ENSG00000158815:transcript:ENST00000328693\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
462 # gene_biotype:protein_coding transcript_biotype:protein_coding
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
463 frame_name = ''
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
464 chromStart = self.chromStart
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
465 chromEnd = self.chromEnd
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
466 strand = 1 if self.strand == '+' else -1
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
467 if frame is not None:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
468 block_sum = sum(self.blockSizes)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
469 offset = (block_sum - frame) % 3
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
470 frame_name = '_' + str(frame + 1)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
471 if self.strand == '+':
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
472 chromStart += frame
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
473 chromEnd -= offset
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
474 else:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
475 chromStart += offset
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
476 chromEnd -= frame
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
477 location = "chromosome:%s:%s:%s:%s:%s"\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
478 % (reference, self.chrom, chromStart, chromEnd, strand)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
479 seq_id = "%s%s %s %s" % (self.name, frame_name, seqtype, location)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
480 return seq_id
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
481
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
482 def get_line(self, start_offset=0, end_offset=0):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
483 if start_offset or end_offset:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
484 s_offset = start_offset if start_offset else 0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
485 e_offset = end_offset if end_offset else 0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
486 if s_offset > self.chromStart:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
487 s_offset = self.chromStart
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
488 chrStart = self.chromStart - s_offset
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
489 chrEnd = self.chromEnd + e_offset
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
490 blkSizes = self.blockSizes
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
491 blkSizes[0] += s_offset
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
492 blkSizes[-1] += e_offset
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
493 blkStarts = self.blockStarts
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
494 for i in range(1, self.blockCount):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
495 blkStarts[i] += s_offset
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
496 items = [str(x) for x in [self.chrom, chrStart, chrEnd, self.name,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
497 self.score, self.strand, self.thickStart,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
498 self.thickEnd, self.itemRgb,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
499 self.blockCount,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
500 ','.join([str(x) for x in blkSizes]),
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
501 ','.join([str(x) for x in blkStarts])]]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
502 return '\t'.join(items) + '\n'
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
parents:
diff changeset
503 return self.line