Mercurial > repos > eric-rasche > apollo
view create_features_from_gff3.py @ 5:7610987e0c48 draft
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
author | eric-rasche |
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date | Wed, 01 Mar 2017 22:39:58 -0500 |
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children | f9a6e151b3b4 |
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#!/usr/bin/env python import sys import json import time import argparse from webapollo import WebApolloInstance, featuresToFeatureSchema from webapollo import WAAuth, OrgOrGuess, GuessOrg, AssertUser from BCBio import GFF import logging logging.basicConfig(level=logging.INFO) log = logging.getLogger(__name__) if __name__ == '__main__': parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services') WAAuth(parser) parser.add_argument('email', help='User Email') OrgOrGuess(parser) parser.add_argument('gff3', type=argparse.FileType('r'), help='GFF3 file') args = parser.parse_args() wa = WebApolloInstance(args.apollo, args.username, args.password) # User must have an account gx_user = AssertUser(wa.users.loadUsers(email=args.email)) # Get organism org_cn = GuessOrg(args, wa) if isinstance(org_cn, list): org_cn = org_cn[0] # TODO: Check user perms on org. org = wa.organisms.findOrganismByCn(org_cn) bad_quals = ['date_creation', 'source', 'owner', 'date_last_modified', 'Name', 'ID'] sys.stdout.write('# ') sys.stdout.write('\t'.join(['Feature ID', 'Apollo ID', 'Success', 'Messages'])) sys.stdout.write('\n') # print(wa.annotations.getFeatures()) for rec in GFF.parse(args.gff3): wa.annotations.setSequence(rec.id, org['id']) for feature in rec.features: # We can only handle genes right now if feature.type != 'gene': continue # Convert the feature into a presentation that Apollo will accept featureData = featuresToFeatureSchema([feature]) try: # We're experiencing a (transient?) problem where gene_001 to # gene_025 will be rejected. Thus, hardcode to a known working # gene name and update later. featureData[0]['name'] = 'gene_000' # Extract CDS feature from the feature data, this will be used # to set the CDS location correctly (apollo currently screwing # this up (2.0.6)) CDS = featureData[0]['children'][0]['children'] CDS = [x for x in CDS if x['type']['name'] == 'CDS'][0]['location'] # Create the new feature newfeature = wa.annotations.addFeature(featureData, trustme=True) # Extract the UUIDs that apollo returns to us mrna_id = newfeature['features'][0]['uniquename'] gene_id = newfeature['features'][0]['parent_id'] # Sleep to give it time to actually persist the feature. Apollo # is terrible about writing + immediately reading back written # data. time.sleep(1) # Correct the translation start, but with strand specific log if CDS['strand'] == 1: wa.annotations.setTranslationStart(mrna_id, min(CDS['fmin'], CDS['fmax'])) else: wa.annotations.setTranslationStart(mrna_id, max(CDS['fmin'], CDS['fmax']) - 1) # Finally we set the name, this should be correct. wa.annotations.setName(mrna_id, feature.qualifiers.get('product', ["Unknown"])[0]) wa.annotations.setName(gene_id, feature.qualifiers.get('product', ["Unknown"])[0]) for (k, v) in feature.qualifiers.items(): if k not in bad_quals: # set qualifier pass sys.stdout.write('\t'.join([ feature.id, gene_id, 'success', "Dropped qualifiers: %s" % (json.dumps({k: v for (k, v) in feature.qualifiers.items() if k not in bad_quals})), ])) except Exception as e: sys.stdout.write('\t'.join([ feature.id, '', 'ERROR', str(e) ])) sys.stdout.write('\n')