Mercurial > repos > gga > apollo_list_organism
view create_features_from_gff3.py @ 8:2c749ed310da draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 2488ac4ea447c45886ce5c7b102fb28c5839d26b
author | gga |
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date | Wed, 10 Apr 2019 14:07:45 -0400 |
parents | a3000d01c04c |
children | bc2b80fc7e30 |
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#!/usr/bin/env python import argparse import logging import sys import time from BCBio import GFF from six.moves.builtins import str from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, WAAuth, WebApolloInstance, featuresToFeatureSchema, retry 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') parser.add_argument('--source', help='URL where the input dataset can be found.') 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 = wa.users.assertOrCreateUser(args.email) # Get organism org_cn = GuessOrg(args, wa) if isinstance(org_cn, list): org_cn = org_cn[0] if not PermissionCheck(gx_user, org_cn, "WRITE"): raise Exception("Action not permitted") 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 not in ('gene', 'terminator'): continue # Convert the feature into a presentation that Apollo will accept featureData = featuresToFeatureSchema([feature]) if 'children' in featureData[0] and any([child['type']['name'] == 'tRNA' for child in featureData[0]['children']]): # 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'] = 'tRNA_000' tRNA_sf = [child for child in feature.sub_features if child.type == 'tRNA'][0] tRNA_type = 'tRNA-' + tRNA_sf.qualifiers.get('Codon', ["Unk"])[0] if 'Name' in feature.qualifiers: if feature.qualifiers['Name'][0].startswith('tRNA-'): tRNA_type = feature.qualifiers['Name'][0] newfeature = wa.annotations.addFeature(featureData, trustme=True) def func0(): wa.annotations.setName( newfeature['features'][0]['uniquename'], tRNA_type, ) retry(func0) if args.source: gene_id = newfeature['features'][0]['parent_id'] def setSource(): wa.annotations.addAttributes(gene_id, {'DatasetSource': [args.source]}) retry(setSource) sys.stdout.write('\t'.join([ feature.id, newfeature['features'][0]['uniquename'], 'success', ])) elif featureData[0]['type']['name'] == 'terminator': # 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'] = 'terminator_000' newfeature = wa.annotations.addFeature(featureData, trustme=True) def func0(): wa.annotations.setName( newfeature['features'][0]['uniquename'], 'terminator' ) retry(func0) if args.source: gene_id = newfeature['features'][0]['parent_id'] def setSource(): wa.annotations.addAttributes(gene_id, {'DatasetSource': [args.source]}) retry(setSource) sys.stdout.write('\t'.join([ feature.id, newfeature['features'][0]['uniquename'], 'success', ])) else: 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. time.sleep(0.5) wa.annotations.setName(mrna_id, feature.qualifiers.get('product', feature.qualifiers.get('Name', ["Unknown"]))[0]) time.sleep(0.5) def func(): wa.annotations.setName(gene_id, feature.qualifiers.get('product', feature.qualifiers.get('Name', ["Unknown"]))[0]) retry(func) if args.source: gene_id = newfeature['features'][0]['parent_id'] def setSource(): wa.annotations.addAttributes(gene_id, {'DatasetSource': [args.source]}) retry(setSource) extra_attr = {} for (key, values) in feature.qualifiers.items(): if key in bad_quals: continue if key == 'Note': def func2(): wa.annotations.addComments(gene_id, values) retry(func2) else: extra_attr[key] = values def func3(): wa.annotations.addAttributes(gene_id, extra_attr) retry(func3) sys.stdout.write('\t'.join([ feature.id, gene_id, 'success', ])) except Exception as e: msg = str(e) if '\n' in msg: msg = msg[0:msg.index('\n')] sys.stdout.write('\t'.join([ feature.id, '', 'ERROR', msg ])) sys.stdout.write('\n') sys.stdout.flush()