Mercurial > repos > iuc > exonerate

annotate exonerategff_to_gff3.py @ 4:37f3a8c3c694 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 08:06:32 +0000
parents 0d6a5769f901
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
iuc
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diff changeset
1 #!/usr/bin/env python3
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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2
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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3 """
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
iuc
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4 Converts a GFF produced by exonerate into a more standard GFF3 (e.g. usable in JBrowse)
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
iuc
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5 """
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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6
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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7 import argparse
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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8 import sys
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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9
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
iuc
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10 from BCBio import GFF
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
iuc
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11 from Bio.SeqFeature import FeatureLocation, SeqFeature
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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12
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
iuc
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13 parser = argparse.ArgumentParser()
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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14 parser.add_argument('infile', nargs='?', type=argparse.FileType('r'), default=sys.stdin)
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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15 parser.add_argument('outfile', nargs='?', type=argparse.FileType('a'), default=sys.stdout)
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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16 args = parser.parse_args()
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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17
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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18
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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19 scaffs = []
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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20 gene_number = 0
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
iuc
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21 for scaff in GFF.parse(args.infile):
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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22 scaff.annotations = {}
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
iuc
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23 scaff.seq = ""
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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24 kept_features = []
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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25 current_gene = None
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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26 exon_number = 0
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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27 last_utr = None
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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28
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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29 for feature in scaff.features:
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30
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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31 if feature.type == "gene":
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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32 gene_number += 1
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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33 mrna_feature = SeqFeature(FeatureLocation(feature.location.start, feature.location.end), type="mRNA", strand=feature.location.strand)
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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34 mrna_feature.sub_features = []
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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35 mrna_feature.qualifiers['source'] = feature.qualifiers['source']
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
iuc
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36 mrna_id = "mRNA_" + str(gene_number)
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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37 mrna_feature.qualifiers['ID'] = mrna_id
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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38 feature.sub_features = [mrna_feature]
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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39 feature.qualifiers['ID'] = "gene_" + str(gene_number)
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
iuc
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40 if 'gene_orientation' in feature.qualifiers:
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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41 del feature.qualifiers['gene_orientation']
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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42 if current_gene:
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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43 kept_features.append(current_gene)
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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44
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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45 current_gene = feature
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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46 exon_number = 0
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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47 last_utr = None
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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48
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49 elif feature.type == 'utr5':
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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50 feature.type = 'five_prime_UTR'
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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51 feature.qualifiers['ID'] = '%s_five_prime_UTR' % (mrna_id)
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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52 mrna_feature.sub_features.append(feature)
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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53 last_utr = {'start': feature.location.start, 'end': feature.location.end}
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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54
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55 elif feature.type == 'utr3':
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56 feature.type = 'three_prime_UTR'
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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57 feature.qualifiers['ID'] = '%s_three_prime_UTR' % (mrna_id)
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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58 mrna_feature.sub_features.append(feature)
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59 last_utr = {'start': feature.location.start, 'end': feature.location.end}
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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60
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61 elif feature.type == 'exon':
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62 exon_number += 1
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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63 feature.qualifiers['ID'] = '%s_exon_%s' % (mrna_id, exon_number)
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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64 mrna_feature.sub_features.append(feature)
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65
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66 if last_utr is None:
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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67 cds_feature = SeqFeature(FeatureLocation(feature.location.start, feature.location.end), type="CDS", strand=feature.location.strand)
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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68 cds_feature.sub_features = []
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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69 cds_feature.qualifiers['source'] = feature.qualifiers['source']
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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70 cds_feature.qualifiers['ID'] = mrna_id + "_CDS"
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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71 mrna_feature.sub_features.append(cds_feature)
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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72 elif feature.location.start != last_utr['start'] or feature.location.end != last_utr['end']:
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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73 if feature.location.start > last_utr['start']:
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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74 cds_feature = SeqFeature(FeatureLocation(feature.location.start, last_utr['start']), type="CDS", strand=feature.location.strand)
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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75 cds_feature.sub_features = []
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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76 cds_feature.qualifiers['source'] = feature.qualifiers['source']
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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77 cds_feature.qualifiers['ID'] = mrna_id + "_CDS"
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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78 mrna_feature.sub_features.append(cds_feature)
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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79 if feature.location.end < last_utr['end']:
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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80 cds_feature = SeqFeature(FeatureLocation(feature.location.end, last_utr['end']), type="CDS", strand=feature.location.strand)
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
iuc
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81 cds_feature.sub_features = []
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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82 cds_feature.qualifiers['source'] = feature.qualifiers['source']
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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83 cds_feature.qualifiers['ID'] = mrna_id + "_CDS"
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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84 mrna_feature.sub_features.append(cds_feature)
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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85
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86 last_utr = None
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87
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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88 elif feature.type == 'similarity':
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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89 if current_gene is None:
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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90 # We haven't seen any gene, just convert similarity to match
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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91 feature.type = 'match'
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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92 kept_features.append(feature)
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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93
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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94 last_utr = None
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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95
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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96 elif feature.type not in ['splice3', 'splice5', 'similarity', 'intron']:
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
iuc
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97 mrna_feature.sub_features.append(feature)
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
iuc
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98 last_utr = None
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
iuc
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99
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
iuc
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100 # For the last one
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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101 if current_gene:
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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102 kept_features.append(current_gene)
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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103
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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104 scaff.features = kept_features
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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105
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
iuc
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106 if len(kept_features):
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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107 GFF.write([scaff], args.outfile)