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annotate delete_features.py @ 0:b4a85d0c85b8 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
author gga
date Mon, 11 Sep 2017 05:47:07 -0400
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children 950fb2bf116d
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b4a85d0c85b8 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
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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 webapollo import AssertUser, GuessOrg, OrgOrGuess, WAAuth, WebApolloInstance, retry
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9 logging.basicConfig(level=logging.INFO)
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10 log = logging.getLogger(__name__)
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13 if __name__ == '__main__':
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14 parser = argparse.ArgumentParser(description='Sample script to delete all features from an organism')
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15 WAAuth(parser)
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16 parser.add_argument('email', help='User Email')
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17 parser.add_argument('--type', help='Feature type filter')
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18 OrgOrGuess(parser)
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20 args = parser.parse_args()
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22 wa = WebApolloInstance(args.apollo, args.username, args.password)
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23 # User must have an account
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24 gx_user = AssertUser(wa.users.loadUsers(email=args.email))
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26 # Get organism
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27 org_cn = GuessOrg(args, wa)
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28 if isinstance(org_cn, list):
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29 org_cn = org_cn[0]
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31 # TODO: Check user perms on org.
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32 org = wa.organisms.findOrganismByCn(org_cn)
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33
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34 sequences = wa.organisms.getSequencesForOrganism(org['id'])
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35 for sequence in sequences['sequences']:
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36 log.info("Processing %s %s", org['commonName'], sequence['name'])
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37 # Call setSequence to tell apollo which organism we're working with
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38 wa.annotations.setSequence(sequence['name'], org['id'])
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39 # Then get a list of features.
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40 features = wa.annotations.getFeatures()
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41 # For each feature in the features
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42 for feature in sorted(features['features'], key=lambda x: random.random()):
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43 if args.type:
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44 if args.type == 'tRNA':
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45 if feature['type']['name'] != 'tRNA':
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46 continue
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47
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48 elif args.type == 'terminator':
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49 if feature['type']['name'] != 'terminator':
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50 continue
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51
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52 elif args.type == 'mRNA':
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53 if feature['type']['name'] != 'mRNA':
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54 continue
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55
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56 else:
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57 raise Exception("Unknown type")
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58
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59 # We see that deleteFeatures wants a uniqueName, and so we pass
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60 # is the uniquename field in the feature.
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61 def fn():
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62 wa.annotations.deleteFeatures([feature['uniquename']])
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63 print('Deleted %s [type=%s]' % (feature['uniquename'], feature['type']['name']))
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64
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65 if not retry(fn, limit=3):
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66 print('Error %s' % feature['uniquename'])