Mercurial > repos > gga > apollo_feat_from_gff3

annotate delete_features.py @ 10:5d1cf95ade8a draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
author gga
date Mon, 02 Dec 2019 05:51:05 -0500
parents cc098732daf6
children
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1 #!/usr/bin/env python
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2 from __future__ import print_function
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4 import argparse
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5 import logging
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6 import random
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8 from apollo import accessible_organisms
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9 from apollo.util import GuessOrg, OrgOrGuess, retry
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11 from arrow.apollo import get_apollo_instance
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13 from webapollo import UserObj, handle_credentials
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15 logging.basicConfig(level=logging.INFO)
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16 log = logging.getLogger(__name__)
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19 if __name__ == '__main__':
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20 parser = argparse.ArgumentParser(description='Script to delete all features from an organism')
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21 parser.add_argument('email', help='User Email')
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22 parser.add_argument('--type', help='Feature type filter')
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23 OrgOrGuess(parser)
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25 args = parser.parse_args()
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27 wa = get_apollo_instance()
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28 # User must have an account
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29 gx_user = UserObj(**wa.users._assert_or_create_user(args.email))
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30 handle_credentials(gx_user)
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32 # Get organism
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33 org_cn = GuessOrg(args, wa)
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34 if isinstance(org_cn, list):
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35 org_cn = org_cn[0]
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36
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37 all_orgs = wa.organisms.get_organisms()
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38 if 'error' in all_orgs:
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39 all_orgs = []
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40 all_orgs = [org['commonName'] for org in all_orgs]
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41 if org_cn not in all_orgs:
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42 raise Exception("Could not find organism %s" % org_cn)
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44 orgs = accessible_organisms(gx_user, [org_cn], 'WRITE')
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45 if not orgs:
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46 raise Exception("You do not have write permission on this organism")
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47 org = wa.organisms.show_organism(org_cn)
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49 sequences = wa.organisms.get_sequences(org['id'])
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50 for sequence in sequences['sequences']:
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51 log.info("Processing %s %s", org['commonName'], sequence['name'])
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52 # Call setSequence to tell apollo which organism we're working with
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53 wa.annotations.set_sequence(org['id'], sequence['name'])
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54 # Then get a list of features.
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55 features = wa.annotations.get_features()
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56 # For each feature in the features
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57 for feature in sorted(features['features'], key=lambda x: random.random()):
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58 if args.type:
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59 if args.type == 'tRNA':
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60 if feature['type']['name'] != 'tRNA':
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61 continue
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63 elif args.type == 'terminator':
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64 if feature['type']['name'] != 'terminator':
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65 continue
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67 elif args.type == 'mRNA':
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68 if feature['type']['name'] != 'mRNA':
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69 continue
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71 else:
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72 raise Exception("Unknown type")
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74 # We see that deleteFeatures wants a uniqueName, and so we pass
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75 # is the uniquename field in the feature.
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76 def fn():
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77 wa.annotations.delete_feature(feature['uniquename'])
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78 print('Deleted %s [type=%s]' % (feature['uniquename'], feature['type']['name']))
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80 if not retry(fn, limit=3):
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81 print('Error %s' % feature['uniquename'])