Mercurial > repos > eric-rasche > apollo

annotate create_features_from_gff3.py @ 8:df7a90763b3c draft default tip

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planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 37aa8fa02c144220da9a3899644025b8c19697c9
author eric-rasche
date Tue, 27 Jun 2017 04:13:27 -0400
parents f9a6e151b3b4
children
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7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
diff changeset
1 #!/usr/bin/env python
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f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 5
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2 from builtins import str
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7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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3 import sys
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
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4 import time
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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5 import argparse
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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6 from webapollo import WebApolloInstance, featuresToFeatureSchema
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f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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7 from webapollo import WAAuth, OrgOrGuess, GuessOrg, AssertUser, retry
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7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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8 from BCBio import GFF
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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9 import logging
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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10 logging.basicConfig(level=logging.INFO)
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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11 log = logging.getLogger(__name__)
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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14 if __name__ == '__main__':
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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15 parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services')
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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16 WAAuth(parser)
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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17 parser.add_argument('email', help='User Email')
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f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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18 parser.add_argument('--source', help='URL where the input dataset can be found.')
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7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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19 OrgOrGuess(parser)
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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21 parser.add_argument('gff3', type=argparse.FileType('r'), help='GFF3 file')
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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22 args = parser.parse_args()
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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24 wa = WebApolloInstance(args.apollo, args.username, args.password)
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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25 # User must have an account
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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26 gx_user = AssertUser(wa.users.loadUsers(email=args.email))
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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28 # Get organism
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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29 org_cn = GuessOrg(args, wa)
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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30 if isinstance(org_cn, list):
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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31 org_cn = org_cn[0]
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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33 # TODO: Check user perms on org.
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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34 org = wa.organisms.findOrganismByCn(org_cn)
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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36 bad_quals = ['date_creation', 'source', 'owner', 'date_last_modified', 'Name', 'ID']
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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38 sys.stdout.write('# ')
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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39 sys.stdout.write('\t'.join(['Feature ID', 'Apollo ID', 'Success', 'Messages']))
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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40 sys.stdout.write('\n')
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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41 # print(wa.annotations.getFeatures())
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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42 for rec in GFF.parse(args.gff3):
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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43 wa.annotations.setSequence(rec.id, org['id'])
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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44 for feature in rec.features:
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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45 # We can only handle genes right now
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f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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46 if feature.type not in ('gene', 'terminator'):
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7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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47 continue
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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48 # Convert the feature into a presentation that Apollo will accept
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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49 featureData = featuresToFeatureSchema([feature])
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f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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parents: 5
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50 if 'children' in featureData[0] and any([child['type']['name'] == 'tRNA' for child in featureData[0]['children']]):
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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parents: 5
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51 # We're experiencing a (transient?) problem where gene_001 to
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
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52 # gene_025 will be rejected. Thus, hardcode to a known working
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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53 # gene name and update later.
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54
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55 featureData[0]['name'] = 'tRNA_000'
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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56 tRNA_sf = [child for child in feature.sub_features if child.type == 'tRNA'][0]
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
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57 tRNA_type = 'tRNA-' + tRNA_sf.qualifiers.get('Codon', ["Unk"])[0]
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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59 if 'Name' in feature.qualifiers:
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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60 if feature.qualifiers['Name'][0].startswith('tRNA-'):
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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61 tRNA_type = feature.qualifiers['Name'][0]
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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63 newfeature = wa.annotations.addFeature(featureData, trustme=True)
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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65 def func0():
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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66 wa.annotations.setName(
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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67 newfeature['features'][0]['uniquename'],
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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68 tRNA_type,
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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69 )
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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70 retry(func0)
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72 if args.source:
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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73 gene_id = newfeature['features'][0]['parent_id']
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74
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75 def setSource():
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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76 wa.annotations.addAttributes(gene_id, {'DatasetSource': [args.source]})
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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77 retry(setSource)
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78
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79 sys.stdout.write('\t'.join([
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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80 feature.id,
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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81 newfeature['features'][0]['uniquename'],
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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82 'success',
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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83 ]))
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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84 elif featureData[0]['type']['name'] == 'terminator':
5
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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85 # We're experiencing a (transient?) problem where gene_001 to
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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86 # gene_025 will be rejected. Thus, hardcode to a known working
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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87 # gene name and update later.
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88 featureData[0]['name'] = 'terminator_000'
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7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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89 newfeature = wa.annotations.addFeature(featureData, trustme=True)
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f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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90
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91 def func0():
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92 wa.annotations.setName(
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93 newfeature['features'][0]['uniquename'],
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94 'terminator'
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95 )
5
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96
7
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97 retry(func0)
5
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98
7
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99 if args.source:
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100 gene_id = newfeature['features'][0]['parent_id']
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101
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102 def setSource():
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103 wa.annotations.addAttributes(gene_id, {'DatasetSource': [args.source]})
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104 retry(setSource)
5
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105
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106 sys.stdout.write('\t'.join([
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107 feature.id,
7
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108 newfeature['features'][0]['uniquename'],
5
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109 'success',
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110 ]))
7
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111 else:
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112 try:
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113 # We're experiencing a (transient?) problem where gene_001 to
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114 # gene_025 will be rejected. Thus, hardcode to a known working
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115 # gene name and update later.
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116 featureData[0]['name'] = 'gene_000'
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117 # Extract CDS feature from the feature data, this will be used
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118 # to set the CDS location correctly (apollo currently screwing
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119 # this up (2.0.6))
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120 CDS = featureData[0]['children'][0]['children']
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121 CDS = [x for x in CDS if x['type']['name'] == 'CDS'][0]['location']
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122 # Create the new feature
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123 newfeature = wa.annotations.addFeature(featureData, trustme=True)
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124 # Extract the UUIDs that apollo returns to us
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125 mrna_id = newfeature['features'][0]['uniquename']
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126 gene_id = newfeature['features'][0]['parent_id']
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127 # Sleep to give it time to actually persist the feature. Apollo
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128 # is terrible about writing + immediately reading back written
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129 # data.
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130 time.sleep(1)
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131 # Correct the translation start, but with strand specific log
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132 if CDS['strand'] == 1:
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133 wa.annotations.setTranslationStart(mrna_id, min(CDS['fmin'], CDS['fmax']))
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134 else:
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135 wa.annotations.setTranslationStart(mrna_id, max(CDS['fmin'], CDS['fmax']) - 1)
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136
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137 # Finally we set the name, this should be correct.
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138 time.sleep(0.5)
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139 wa.annotations.setName(mrna_id, feature.qualifiers.get('product', feature.qualifiers.get('Name', ["Unknown"]))[0])
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140 time.sleep(0.5)
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141
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142 def func():
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143 wa.annotations.setName(gene_id, feature.qualifiers.get('product', feature.qualifiers.get('Name', ["Unknown"]))[0])
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144 retry(func)
5
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145
7
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146 if args.source:
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147 gene_id = newfeature['features'][0]['parent_id']
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148
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149 def setSource():
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150 wa.annotations.addAttributes(gene_id, {'DatasetSource': [args.source]})
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151 retry(setSource)
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152 extra_attr = {}
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153 for (key, values) in feature.qualifiers.items():
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154 if key in bad_quals:
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155 continue
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156
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157 if key == 'Note':
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158 def func2():
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159 wa.annotations.addComments(gene_id, values)
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160 retry(func2)
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161 else:
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162 extra_attr[key] = values
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163
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164 def func3():
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165 wa.annotations.addAttributes(gene_id, extra_attr)
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166 retry(func3)
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167
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168 sys.stdout.write('\t'.join([
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169 feature.id,
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170 gene_id,
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171 'success',
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172 ]))
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173 except Exception as e:
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174 msg = str(e)
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175 if '\n' in msg:
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176 msg = msg[0:msg.index('\n')]
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177 sys.stdout.write('\t'.join([
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178 feature.id,
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179 '',
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180 'ERROR',
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181 msg
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 5
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182 ]))
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7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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183 sys.stdout.write('\n')
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f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 5
diff changeset
184 sys.stdout.flush()