Mercurial > repos > gga > apollo_fetch_jbrowse
annotate create_features_from_gff3.py @ 6:54277b911534 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit d9f27b297d9a919471c92b02ecf6cc9554457211
author | gga |
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date | Tue, 30 Oct 2018 04:31:11 -0400 |
parents | 1a2976c6b161 |
children | dca2fb399ee6 |
rev | line source |
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c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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1 #!/usr/bin/env python |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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2 import argparse |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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3 import logging |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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4 import sys |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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5 import time |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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6 |
4
9968eec7430e
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 70fbb41d4c6b0a08a7bed4849a5ae7c865e1ab1e
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7 from BCBio import GFF |
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c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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8 |
4
9968eec7430e
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 70fbb41d4c6b0a08a7bed4849a5ae7c865e1ab1e
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9 from six.moves.builtins import str |
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c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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10 |
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1a2976c6b161
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
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11 from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, WAAuth, WebApolloInstance, featuresToFeatureSchema, retry |
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c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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12 logging.basicConfig(level=logging.INFO) |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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13 log = logging.getLogger(__name__) |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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14 |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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15 |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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16 if __name__ == '__main__': |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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17 parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services') |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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18 WAAuth(parser) |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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19 parser.add_argument('email', help='User Email') |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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20 parser.add_argument('--source', help='URL where the input dataset can be found.') |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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21 OrgOrGuess(parser) |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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22 |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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23 parser.add_argument('gff3', type=argparse.FileType('r'), help='GFF3 file') |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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24 args = parser.parse_args() |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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25 |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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26 wa = WebApolloInstance(args.apollo, args.username, args.password) |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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27 # User must have an account |
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1a2976c6b161
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
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28 gx_user = wa.users.assertOrCreateUser(args.email) |
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c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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29 |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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30 # Get organism |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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31 org_cn = GuessOrg(args, wa) |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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32 if isinstance(org_cn, list): |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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33 org_cn = org_cn[0] |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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34 |
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1a2976c6b161
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
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35 if not PermissionCheck(gx_user, org_cn, "WRITE"): |
1a2976c6b161
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
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36 raise Exception("Action not permitted") |
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c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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37 org = wa.organisms.findOrganismByCn(org_cn) |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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38 |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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39 bad_quals = ['date_creation', 'source', 'owner', 'date_last_modified', 'Name', 'ID'] |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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40 |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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41 sys.stdout.write('# ') |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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42 sys.stdout.write('\t'.join(['Feature ID', 'Apollo ID', 'Success', 'Messages'])) |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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43 sys.stdout.write('\n') |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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44 # print(wa.annotations.getFeatures()) |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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45 for rec in GFF.parse(args.gff3): |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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46 wa.annotations.setSequence(rec.id, org['id']) |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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47 for feature in rec.features: |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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48 # We can only handle genes right now |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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49 if feature.type not in ('gene', 'terminator'): |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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50 continue |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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51 # Convert the feature into a presentation that Apollo will accept |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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52 featureData = featuresToFeatureSchema([feature]) |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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53 if 'children' in featureData[0] and any([child['type']['name'] == 'tRNA' for child in featureData[0]['children']]): |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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54 # We're experiencing a (transient?) problem where gene_001 to |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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55 # gene_025 will be rejected. Thus, hardcode to a known working |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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56 # gene name and update later. |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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57 |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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58 featureData[0]['name'] = 'tRNA_000' |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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59 tRNA_sf = [child for child in feature.sub_features if child.type == 'tRNA'][0] |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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60 tRNA_type = 'tRNA-' + tRNA_sf.qualifiers.get('Codon', ["Unk"])[0] |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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61 |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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62 if 'Name' in feature.qualifiers: |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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63 if feature.qualifiers['Name'][0].startswith('tRNA-'): |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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64 tRNA_type = feature.qualifiers['Name'][0] |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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65 |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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66 newfeature = wa.annotations.addFeature(featureData, trustme=True) |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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67 |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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68 def func0(): |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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69 wa.annotations.setName( |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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70 newfeature['features'][0]['uniquename'], |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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71 tRNA_type, |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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72 ) |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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73 retry(func0) |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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74 |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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75 if args.source: |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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76 gene_id = newfeature['features'][0]['parent_id'] |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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77 |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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78 def setSource(): |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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79 wa.annotations.addAttributes(gene_id, {'DatasetSource': [args.source]}) |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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80 retry(setSource) |
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81 |
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82 sys.stdout.write('\t'.join([ |
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83 feature.id, |
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84 newfeature['features'][0]['uniquename'], |
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85 'success', |
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86 ])) |
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87 elif featureData[0]['type']['name'] == 'terminator': |
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88 # We're experiencing a (transient?) problem where gene_001 to |
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89 # gene_025 will be rejected. Thus, hardcode to a known working |
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90 # gene name and update later. |
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91 featureData[0]['name'] = 'terminator_000' |
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92 newfeature = wa.annotations.addFeature(featureData, trustme=True) |
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93 |
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94 def func0(): |
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95 wa.annotations.setName( |
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96 newfeature['features'][0]['uniquename'], |
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97 'terminator' |
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98 ) |
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99 |
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100 retry(func0) |
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101 |
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102 if args.source: |
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103 gene_id = newfeature['features'][0]['parent_id'] |
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104 |
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105 def setSource(): |
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106 wa.annotations.addAttributes(gene_id, {'DatasetSource': [args.source]}) |
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107 retry(setSource) |
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108 |
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109 sys.stdout.write('\t'.join([ |
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110 feature.id, |
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111 newfeature['features'][0]['uniquename'], |
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112 'success', |
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113 ])) |
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114 else: |
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115 try: |
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116 # We're experiencing a (transient?) problem where gene_001 to |
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117 # gene_025 will be rejected. Thus, hardcode to a known working |
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118 # gene name and update later. |
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119 featureData[0]['name'] = 'gene_000' |
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120 # Extract CDS feature from the feature data, this will be used |
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121 # to set the CDS location correctly (apollo currently screwing |
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122 # this up (2.0.6)) |
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123 CDS = featureData[0]['children'][0]['children'] |
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124 CDS = [x for x in CDS if x['type']['name'] == 'CDS'][0]['location'] |
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125 # Create the new feature |
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126 newfeature = wa.annotations.addFeature(featureData, trustme=True) |
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127 # Extract the UUIDs that apollo returns to us |
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128 mrna_id = newfeature['features'][0]['uniquename'] |
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129 gene_id = newfeature['features'][0]['parent_id'] |
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130 # Sleep to give it time to actually persist the feature. Apollo |
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131 # is terrible about writing + immediately reading back written |
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132 # data. |
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133 time.sleep(1) |
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134 # Correct the translation start, but with strand specific log |
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135 if CDS['strand'] == 1: |
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136 wa.annotations.setTranslationStart(mrna_id, min(CDS['fmin'], CDS['fmax'])) |
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137 else: |
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138 wa.annotations.setTranslationStart(mrna_id, max(CDS['fmin'], CDS['fmax']) - 1) |
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139 |
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140 # Finally we set the name, this should be correct. |
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141 time.sleep(0.5) |
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142 wa.annotations.setName(mrna_id, feature.qualifiers.get('product', feature.qualifiers.get('Name', ["Unknown"]))[0]) |
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143 time.sleep(0.5) |
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144 |
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145 def func(): |
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146 wa.annotations.setName(gene_id, feature.qualifiers.get('product', feature.qualifiers.get('Name', ["Unknown"]))[0]) |
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147 retry(func) |
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148 |
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149 if args.source: |
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150 gene_id = newfeature['features'][0]['parent_id'] |
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151 |
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152 def setSource(): |
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153 wa.annotations.addAttributes(gene_id, {'DatasetSource': [args.source]}) |
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154 retry(setSource) |
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155 extra_attr = {} |
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156 for (key, values) in feature.qualifiers.items(): |
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157 if key in bad_quals: |
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158 continue |
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159 |
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160 if key == 'Note': |
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161 def func2(): |
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162 wa.annotations.addComments(gene_id, values) |
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163 retry(func2) |
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164 else: |
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165 extra_attr[key] = values |
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166 |
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167 def func3(): |
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168 wa.annotations.addAttributes(gene_id, extra_attr) |
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169 retry(func3) |
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170 |
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171 sys.stdout.write('\t'.join([ |
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172 feature.id, |
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173 gene_id, |
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174 'success', |
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175 ])) |
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176 except Exception as e: |
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177 msg = str(e) |
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178 if '\n' in msg: |
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179 msg = msg[0:msg.index('\n')] |
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180 sys.stdout.write('\t'.join([ |
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181 feature.id, |
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182 '', |
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183 'ERROR', |
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184 msg |
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185 ])) |
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186 sys.stdout.write('\n') |
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187 sys.stdout.flush() |