Mercurial > repos > iuc > deg_annotate

annotate deg_annotate.py @ 2:e81fbbea6e8f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit f926103056cdcd0c37c38f7c636870e5b1f9f8c5
author iuc
date Sat, 21 Jun 2025 13:03:14 +0000
parents e98d4ab5b5bc
children
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b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
parents:
diff changeset
1 import argparse
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
parents:
diff changeset
2 import os
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
parents:
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3 from collections import defaultdict
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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4
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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5 from BCBio import GFF
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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6
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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7
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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8 def strandardize(strand):
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
parents:
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9 if str(strand) == '-1':
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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10 strand = '-'
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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11 elif str(strand) == '1':
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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12 strand = '+'
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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13 return strand
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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14
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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16 def gff_to_dict(f_gff, feat_type, idattr, txattr, attributes, input_type):
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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17 """
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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18 It reads only exonic features because not all GFF files contain gene and trascript features. From the exonic
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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19 features it extracts gene names, biotypes, start and end positions. If any of these attributes do not exit
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
parents:
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20 then they are set to NA.
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
parents:
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21 """
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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22 annotation = defaultdict(lambda: defaultdict(lambda: 'NA'))
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
parents:
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23 exon_pos = defaultdict(lambda: defaultdict(lambda: defaultdict(int)))
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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24 tx_info = defaultdict(lambda: defaultdict(str))
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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25
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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26 with open(f_gff) as gff_handle:
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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27 for rec in GFF.parse(gff_handle, limit_info=dict(gff_type=[feat_type]), target_lines=1):
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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28 for sub_feature in rec.features:
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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29 start = sub_feature.location.start
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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30 end = sub_feature.location.end
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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31 strand = strandardize(sub_feature.location.strand)
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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32 try:
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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33 geneid = sub_feature.qualifiers[idattr][0]
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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34 except KeyError:
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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35 print("No '" + idattr + "' attribute found for the feature at position "
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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36 + rec.id + ":" + str(start) + ":" + str(end) + ". Please check your GTF/GFF file.")
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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37 continue
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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38
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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39 annotation[geneid]['chr'] = rec.id
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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40 annotation[geneid]['strand'] = strand
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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41 if annotation[geneid]['start'] == 'NA' or start <= int(annotation[geneid]['start']):
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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42 annotation[geneid]['start'] = start
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
parents:
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43 if annotation[geneid]['end'] == 'NA' or end >= int(annotation[geneid]['end']):
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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44 annotation[geneid]['end'] = end
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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45
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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46 for attr in attributes:
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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47 if attr in annotation[geneid]:
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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48 continue
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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49 try:
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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50 annotation[geneid][attr] = sub_feature.qualifiers[attr][0]
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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51 except KeyError:
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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52 annotation[geneid][attr] = 'NA'
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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53 # extract exon information only in case of dexseq output
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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54 if input_type != "dexseq":
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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55 continue
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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56 try:
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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57 txid = sub_feature.qualifiers[txattr][0]
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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58 tx_info[txid]['chr'] = rec.id
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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59 tx_info[txid]['strand'] = strand
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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60 exon_pos[txid][int(start)][int(end)] = 1
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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61 except KeyError:
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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62 print("No '" + txattr + "' attribute found for the feature at position " + rec.id + ":" + str(
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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63 start) + ":" + str(end) + ". Please check your GTF/GFF file.")
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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64 pass
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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65
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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66 bed_entries = []
1
e98d4ab5b5bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit 44d3dae188cabf4a64dee7c1ebe41c855d95d1b0
iuc
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67 # create BED lines only for dexeq output
0
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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68 if input_type == "dexseq":
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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69 for txid in exon_pos.keys():
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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70 starts = sorted(exon_pos[txid])
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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71 strand = tx_info[txid]['strand']
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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72 if strand == '-':
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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73 starts = reversed(starts)
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
parents:
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74 for c, start in enumerate(starts, 1):
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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75 ends = sorted(exon_pos[txid][start])
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
parents:
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76 if strand == '-':
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
parents:
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77 ends = reversed(ends)
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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78 for end in ends:
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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79 bed_entries.append('\t'.join([tx_info[txid]['chr'], str(start), str(end),
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
parents:
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80 txid + ':' + str(c), '0', strand]))
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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81
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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82 return annotation, bed_entries
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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83
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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84
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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85 def main():
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
parents:
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86 parser = argparse.ArgumentParser(description='Annotate DESeq2/DEXSeq tables with information from GFF/GTF files')
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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87 parser.add_argument('-in', '--input', required=True,
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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88 help='DESeq2/DEXSeq output. It is allowed to have extra information, '
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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89 'but make sure that the original output columns are not altered')
1
e98d4ab5b5bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit 44d3dae188cabf4a64dee7c1ebe41c855d95d1b0
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parents: 0
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90 parser.add_argument('-m', '--mode', required=True, choices=["degseq", "dexseq"],
e98d4ab5b5bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit 44d3dae188cabf4a64dee7c1ebe41c855d95d1b0
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91 default='degseq', help='Input file type')
0
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92 parser.add_argument('-g', '--gff', required=True, help='The same annotation GFF/GTF file used for couting')
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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93 parser.add_argument('-t', '--type', default='exon', required=False,
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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94 help='feature type (3rd column in GFF file) to be used (default: exon)')
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95 parser.add_argument('-i', '--idattr', default='gene_id', required=False,
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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96 help='GFF attribute to be used as feature ID. '
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97 'This should match the first column of DESeq2 output(default: geneid)')
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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98 parser.add_argument('-x', '--txattr', default='transcript_id', required=False,
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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99 help='GFF attribute to be used as transcript ID. Used for DEXSeq output only.'
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100 'This should match the first column of DESeq2 output(default: transcript_id)')
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101 parser.add_argument('-a', '--attributes', default='gene_biotype, gene_name', required=False,
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102 help='Comma separated attributes to include in output. Default: gene_biotype, gene_name')
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103 parser.add_argument('-o', '--output', required=True, help='Output file')
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104 args = parser.parse_args()
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105
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106 print("DE(X)Seq output file : %s" % args.input)
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107 print("Input file type : %s" % args.mode)
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108 print("Annotation file : %s" % args.gff)
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109 print("Feature type : %s" % args.type)
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110 print("ID attribute : %s" % args.idattr)
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111 print("Transcript attribute : %s" % args.txattr)
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112 print("Attributes to include : %s" % args.attributes)
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113 print("Annotated output file : %s" % args.output)
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114
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115 attr = [x.strip() for x in args.attributes.split(',')]
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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116 annotation, bed_entries = gff_to_dict(args.gff, args.type, args.idattr, args.txattr, attr, args.mode)
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117
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118 d_binexon = {}
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119 skip_exon_annotation = False
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120
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121 if args.mode == "dexseq":
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122 with open(args.input) as fh_input, open("input.bed", "w") as fh_input_bed:
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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123 for line in fh_input:
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124 f = line.split('\t')
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125 fh_input_bed.write('\t'.join([f[11], f[12], f[13], f[0], "0", f[15]]) + "\n")
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126
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127 if len(bed_entries) == 0 and args.mode == "dexseq":
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128 print("It seems there are no transcript ids present in GFF file. Skipping exon annotation.")
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129 skip_exon_annotation = True
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130
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131 if not skip_exon_annotation:
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132 with open("annotation.bed", "w") as fh_annotation_bed:
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133 for line in bed_entries:
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134 fh_annotation_bed.write(line + "\n")
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135
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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136 # interset the DEXseq couting bins with exons in the GFF file
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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137 # overlaped positions can be later used to infer which bin corresponds to which exon
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138 os.system("intersectBed -wo -s -a input.bed -b annotation.bed > overlap.txt")
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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139
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140 with open("overlap.txt") as fh_overlap:
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141 for line in fh_overlap:
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142 binid = line.split('\t')[3]
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143 exonid = line.split('\t')[9]
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144 d_binexon.setdefault(binid, []).append(exonid)
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145
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146 with open(args.input) as fh_input, open(args.output, 'w') as fh_output:
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147 for line in fh_input:
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148 annot = []
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149 # DEXSeq exonic bins might originate from aggrigating multiple genes. They are are separated by '+'
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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150 # Append the attributes from the GFF but keep the order of the aggregated genes and use '+'
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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151 # Aappend the transcript id and exon number from the annotation that correspond to the DEXseq counting bins
1
e98d4ab5b5bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit 44d3dae188cabf4a64dee7c1ebe41c855d95d1b0
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152 if args.mode == "dexseq":
0
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153 geneids = line.split('\t')[1].split('+')
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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154 for a in attr:
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diff changeset
155 tmp = []
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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156 for geneid in geneids:
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157 tmp.append(str(annotation[geneid][a]))
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158 annot.append('+'.join(tmp))
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159 if not skip_exon_annotation:
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160 binid = line.split('\t')[0]
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iuc
parents:
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161 try:
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
iuc
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162 annot.append(','.join(sorted(set(d_binexon[binid]))))
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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parents:
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163 except KeyError:
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164 annot.append('NA')
1
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165 # Append the extra information from GFF to DESeq2/edgeR/limma output
e98d4ab5b5bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit 44d3dae188cabf4a64dee7c1ebe41c855d95d1b0
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166 else:
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167 geneid = line.split('\t')[0]
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168 annot = [str(annotation[geneid]['chr']),
e98d4ab5b5bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit 44d3dae188cabf4a64dee7c1ebe41c855d95d1b0
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169 str(annotation[geneid]['start']),
e98d4ab5b5bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit 44d3dae188cabf4a64dee7c1ebe41c855d95d1b0
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170 str(annotation[geneid]['end']),
e98d4ab5b5bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit 44d3dae188cabf4a64dee7c1ebe41c855d95d1b0
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171 str(annotation[geneid]['strand'])]
e98d4ab5b5bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit 44d3dae188cabf4a64dee7c1ebe41c855d95d1b0
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172 for a in attr:
e98d4ab5b5bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit 44d3dae188cabf4a64dee7c1ebe41c855d95d1b0
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173 annot.append(annotation[geneid][a])
0
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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174 fh_output.write(line.rstrip('\n') + '\t' + '\t'.join(annot) + '\n')
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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175
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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176
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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177 if __name__ == "__main__":
b42373cddb77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit bc766aeec78fe74a1d70d608d2f73ba3f2a3e047
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178 main()