Mercurial > repos > iuc > jbrowse
annotate blastxml_to_gapped_gff3.py @ 18:836d1aa3e89a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
author | iuc |
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date | Thu, 16 Nov 2017 09:44:45 -0500 |
parents | ff11d442feed |
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rev | line source |
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18be2d72fdee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
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1 #!/usr/bin/env python |
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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2 import argparse |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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3
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3 import copy |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
3
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4 import logging |
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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changeset
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5 import re |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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changeset
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6 import sys |
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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3
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7 |
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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8 from BCBio import GFF |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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9 logging.basicConfig(level=logging.INFO) |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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10 log = logging.getLogger(name='blastxml2gff3') |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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11 |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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12 __doc__ = """ |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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13 BlastXML files, when transformed to GFF3, do not normally show gaps in the |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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14 blast hits. This tool aims to fill that "gap". |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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15 """ |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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16 |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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17 |
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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18 def blastxml2gff3(blastxml, min_gap=3, trim=False, trim_end=False, include_seq=False): |
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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19 from Bio.Blast import NCBIXML |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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20 from Bio.Seq import Seq |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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21 from Bio.SeqRecord import SeqRecord |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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22 from Bio.SeqFeature import SeqFeature, FeatureLocation |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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23 |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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24 blast_records = NCBIXML.parse(blastxml) |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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25 for idx_record, record in enumerate(blast_records): |
3 | 26 # http://www.sequenceontology.org/browser/release_2.4/term/SO:0000343 |
27 match_type = { # Currently we can only handle BLASTN, BLASTP | |
28 'BLASTN': 'nucleotide_match', | |
29 'BLASTP': 'protein_match', | |
30 }.get(record.application, 'match') | |
31 | |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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32 recid = record.query |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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14
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33 if ' ' in recid: |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
14
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34 recid = recid[0:recid.index(' ')] |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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14
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35 |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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36 rec = SeqRecord(Seq("ACTG"), id=recid) |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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14
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37 for idx_hit, hit in enumerate(record.alignments): |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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38 for idx_hsp, hsp in enumerate(hit.hsps): |
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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39 qualifiers = { |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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40 "ID": 'b2g.%s.%s.%s' % (idx_record, idx_hit, idx_hsp), |
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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41 "source": "blast", |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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42 "score": hsp.expect, |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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43 "accession": hit.accession, |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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44 "hit_id": hit.hit_id, |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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45 "length": hit.length, |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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46 "hit_titles": hit.title.split(' >'), |
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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47 } |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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48 if include_seq: |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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49 qualifiers.update({ |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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50 'blast_qseq': hsp.query, |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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51 'blast_sseq': hsp.sbjct, |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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52 'blast_mseq': hsp.match, |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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53 }) |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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54 |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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55 for prop in ('score', 'bits', 'identities', 'positives', |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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56 'gaps', 'align_length', 'strand', 'frame', |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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57 'query_start', 'query_end', 'sbjct_start', |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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58 'sbjct_end'): |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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59 qualifiers['blast_' + prop] = getattr(hsp, prop, None) |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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60 |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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61 desc = hit.title.split(' >')[0] |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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62 qualifiers['description'] = desc[desc.index(' '):] |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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63 |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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64 # This required a fair bit of sketching out/match to figure out |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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65 # the first time. |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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66 # |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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67 # the match_start location must account for queries and |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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68 # subjecst that start at locations other than 1 |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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69 parent_match_start = hsp.query_start - hsp.sbjct_start |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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70 # The end is the start + hit.length because the match itself |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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71 # may be longer than the parent feature, so we use the supplied |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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72 # subject/hit length to calculate the real ending of the target |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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73 # protein. |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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74 parent_match_end = hsp.query_start + hit.length + hsp.query.count('-') |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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75 |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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76 # If we trim the left end, we need to trim without losing information. |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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77 used_parent_match_start = parent_match_start |
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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78 if trim: |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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79 if parent_match_start < 1: |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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80 used_parent_match_start = 0 |
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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81 |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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82 if trim or trim_end: |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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83 if parent_match_end > hsp.query_end: |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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84 parent_match_end = hsp.query_end + 1 |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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85 |
3 | 86 # The ``match`` feature will hold one or more ``match_part``s |
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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87 top_feature = SeqFeature( |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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88 FeatureLocation(used_parent_match_start, parent_match_end), |
3 | 89 type=match_type, strand=0, |
1
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90 qualifiers=qualifiers |
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91 ) |
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92 |
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93 # Unlike the parent feature, ``match_part``s have sources. |
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94 part_qualifiers = { |
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95 "source": "blast", |
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96 } |
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97 top_feature.sub_features = [] |
17
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98 for idx_part, (start, end, cigar) in \ |
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99 enumerate(generate_parts(hsp.query, hsp.match, |
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100 hsp.sbjct, |
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101 ignore_under=min_gap)): |
1
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102 part_qualifiers['Gap'] = cigar |
17
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103 part_qualifiers['ID'] = qualifiers['ID'] + ('.%s' % idx_part) |
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104 |
17
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105 # Otherwise, we have to account for the subject start's location |
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106 match_part_start = parent_match_start + hsp.sbjct_start + start - 1 |
1
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107 |
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108 # We used to use hsp.align_length here, but that includes |
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109 # gaps in the parent sequence |
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110 # |
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111 # Furthermore align_length will give calculation errors in weird places |
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112 # So we just use (end-start) for simplicity |
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113 match_part_end = match_part_start + (end - start) |
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114 |
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115 top_feature.sub_features.append( |
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116 SeqFeature( |
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117 FeatureLocation(match_part_start, match_part_end), |
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118 type="match_part", strand=0, |
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119 qualifiers=copy.deepcopy(part_qualifiers)) |
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120 ) |
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121 |
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122 rec.features.append(top_feature) |
3 | 123 rec.annotations = {} |
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124 yield rec |
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125 |
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126 |
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127 def __remove_query_gaps(query, match, subject): |
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128 """remove positions in all three based on gaps in query |
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129 |
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130 In order to simplify math and calculations...we remove all of the gaps |
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131 based on gap locations in the query sequence:: |
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132 |
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133 Q:ACTG-ACTGACTG |
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134 S:ACTGAAC---CTG |
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135 |
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136 will become:: |
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137 |
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138 Q:ACTGACTGACTG |
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139 S:ACTGAC---CTG |
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140 |
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141 which greatly simplifies the process of identifying the correct location |
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142 for a match_part |
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143 """ |
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144 prev = 0 |
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145 fq = '' |
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146 fm = '' |
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147 fs = '' |
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148 for position in re.finditer('-', query): |
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149 fq += query[prev:position.start()] |
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150 fm += match[prev:position.start()] |
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151 fs += subject[prev:position.start()] |
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152 prev = position.start() + 1 |
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153 fq += query[prev:] |
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154 fm += match[prev:] |
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155 fs += subject[prev:] |
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156 |
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157 return (fq, fm, fs) |
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158 |
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159 |
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160 def generate_parts(query, match, subject, ignore_under=3): |
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161 region_q = [] |
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162 region_m = [] |
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163 region_s = [] |
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164 |
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165 (query, match, subject) = __remove_query_gaps(query, match, subject) |
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166 |
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167 region_start = -1 |
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168 region_end = -1 |
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169 mismatch_count = 0 |
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170 for i, (q, m, s) in enumerate(zip(query, match, subject)): |
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171 |
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172 # If we have a match |
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173 if m != ' ' or m == '+': |
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174 if region_start == -1: |
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175 region_start = i |
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176 # It's a new region, we need to reset or it's pre-seeded with |
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177 # spaces |
497c6bb3b717
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178 region_q = [] |
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179 region_m = [] |
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180 region_s = [] |
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181 region_end = i |
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182 mismatch_count = 0 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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183 else: |
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184 mismatch_count += 1 |
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185 |
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186 region_q.append(q) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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187 region_m.append(m) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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188 region_s.append(s) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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189 |
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190 if mismatch_count >= ignore_under and region_start != -1 and region_end != -1: |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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191 region_q = region_q[0:-ignore_under] |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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192 region_m = region_m[0:-ignore_under] |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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193 region_s = region_s[0:-ignore_under] |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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194 yield region_start, region_end + 1, \ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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195 cigar_from_string(region_q, region_m, region_s, strict_m=True) |
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196 region_q = [] |
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197 region_m = [] |
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198 region_s = [] |
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199 |
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200 region_start = -1 |
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201 region_end = -1 |
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202 mismatch_count = 0 |
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203 |
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204 yield region_start, region_end + 1, \ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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205 cigar_from_string(region_q, region_m, region_s, strict_m=True) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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206 |
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207 |
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208 def _qms_to_matches(query, match, subject, strict_m=True): |
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209 matchline = [] |
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210 |
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211 for (q, m, s) in zip(query, match, subject): |
497c6bb3b717
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212 ret = '' |
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213 |
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214 if m != ' ' or m == '+': |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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215 ret = '=' |
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216 elif m == ' ': |
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217 if q == '-': |
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218 ret = 'D' |
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219 elif s == '-': |
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220 ret = 'I' |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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221 else: |
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222 ret = 'X' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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223 else: |
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224 log.warn("Bad data: \n\t%s\n\t%s\n\t%s\n" % (query, match, subject)) |
497c6bb3b717
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225 |
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226 if strict_m: |
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227 if ret == '=' or ret == 'X': |
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228 ret = 'M' |
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229 |
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230 matchline.append(ret) |
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231 return matchline |
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232 |
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233 |
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234 def _matchline_to_cigar(matchline): |
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235 cigar_line = [] |
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236 last_char = matchline[0] |
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237 count = 0 |
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238 for char in matchline: |
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239 if char == last_char: |
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240 count += 1 |
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241 else: |
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242 cigar_line.append("%s%s" % (last_char, count)) |
497c6bb3b717
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243 count = 1 |
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244 last_char = char |
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245 cigar_line.append("%s%s" % (last_char, count)) |
497c6bb3b717
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246 return ' '.join(cigar_line) |
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247 |
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248 |
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249 def cigar_from_string(query, match, subject, strict_m=True): |
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250 matchline = _qms_to_matches(query, match, subject, strict_m=strict_m) |
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251 if len(matchline) > 0: |
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252 return _matchline_to_cigar(matchline) |
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253 else: |
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254 return "" |
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255 |
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256 |
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257 if __name__ == '__main__': |
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258 parser = argparse.ArgumentParser(description='Convert Blast XML to gapped GFF3', epilog='') |
17
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259 parser.add_argument('blastxml', type=argparse.FileType("r"), help='Blast XML Output') |
1
497c6bb3b717
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260 parser.add_argument('--min_gap', type=int, help='Maximum gap size before generating a new match_part', default=3) |
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261 parser.add_argument('--trim', action='store_true', help='Trim blast hits to be only as long as the parent feature') |
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262 parser.add_argument('--trim_end', action='store_true', help='Cut blast results off at end of gene') |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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263 parser.add_argument('--include_seq', action='store_true', help='Include sequence') |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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264 args = parser.parse_args() |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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265 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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266 for rec in blastxml2gff3(**vars(args)): |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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267 if len(rec.features): |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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268 GFF.write([rec], sys.stdout) |