Mercurial > repos > gga > apollo_feat_from_gff3

comparison export.py @ 16:12ebb583b8a3 draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
author gga
date Fri, 10 Dec 2021 09:52:37 +0000
parents bb562d95b6cd
children
comparison
equal deleted inserted replaced
15:18217f8862ef 16:12ebb583b8a3
14 14
15 if __name__ == '__main__': 15 if __name__ == '__main__':
16 parser = argparse.ArgumentParser(description='Script to export data from Apollo via web services') 16 parser = argparse.ArgumentParser(description='Script to export data from Apollo via web services')
17 CnOrGuess(parser) 17 CnOrGuess(parser)
18 parser.add_argument('--gff', type=argparse.FileType('w')) 18 parser.add_argument('--gff', type=argparse.FileType('w'))
19 parser.add_argument('--gff_with_fasta', action='store_true')
19 parser.add_argument('--fasta_pep', type=argparse.FileType('w')) 20 parser.add_argument('--fasta_pep', type=argparse.FileType('w'))
20 parser.add_argument('--fasta_cds', type=argparse.FileType('w')) 21 parser.add_argument('--fasta_cds', type=argparse.FileType('w'))
21 parser.add_argument('--fasta_cdna', type=argparse.FileType('w')) 22 parser.add_argument('--fasta_cdna', type=argparse.FileType('w'))
22 parser.add_argument('--vcf', type=argparse.FileType('w')) 23 parser.add_argument('--vcf', type=argparse.FileType('w'))
23 parser.add_argument('--json', type=argparse.FileType('w')) 24 parser.add_argument('--json', type=argparse.FileType('w'))
25 parser.add_argument('--die', action='store_true')
24 parser.add_argument('email', help='User Email') 26 parser.add_argument('email', help='User Email')
25 args = parser.parse_args() 27 args = parser.parse_args()
26 28
27 wa = get_apollo_instance() 29 wa = get_apollo_instance()
28 30
37 all_orgs = wa.organisms.get_organisms() 39 all_orgs = wa.organisms.get_organisms()
38 if 'error' in all_orgs: 40 if 'error' in all_orgs:
39 all_orgs = [] 41 all_orgs = []
40 all_orgs = [org['commonName'] for org in all_orgs] 42 all_orgs = [org['commonName'] for org in all_orgs]
41 43
44 def error(message):
45 if args.die:
46 raise Exception(message)
47 else:
48 print(message)
49
42 org_data = [] 50 org_data = []
43 for org_cn in org_cns: 51 for org_cn in org_cns:
44 if org_cn not in all_orgs: 52 if org_cn not in all_orgs:
45 raise Exception("Could not find organism %s" % org_cn) 53 raise Exception("Could not find organism %s" % org_cn)
46 54
48 if not orgs: 56 if not orgs:
49 raise Exception("You do not have read permission on organism %s" % org_cn) 57 raise Exception("You do not have read permission on organism %s" % org_cn)
50 58
51 org = wa.organisms.show_organism(org_cn) 59 org = wa.organisms.show_organism(org_cn)
52 60
53 uuid_gff = wa.io.write_downloadable(org['commonName'], 'GFF3', export_gff3_fasta=True, sequences=seqs) 61 # Fetch all the refseqs
54 if 'error' in uuid_gff or 'uuid' not in uuid_gff: 62 realSeqs = wa.organisms.get_sequences(org['id'])
55 raise Exception("Apollo failed to prepare the GFF3 file for download: %s" % uuid_gff)
56 args.gff.write(wa.io.download(uuid_gff['uuid'], output_format="text"))
57 63
58 time.sleep(1) 64 # We'll loop over them individually for decreased memory pressure
65 for sequence in realSeqs['sequences']:
66 print("Downloading", sequence)
59 67
60 uuid_vcf = wa.io.write_downloadable(org['commonName'], 'VCF', sequences=seqs) 68 try:
61 if 'error' in uuid_vcf or 'uuid' not in uuid_vcf: 69 uuid_gff = wa.io.write_downloadable(org['commonName'], 'GFF3', export_gff3_fasta=args.gff_with_fasta, sequences=[sequence['name']])
62 raise Exception("Apollo failed to prepare the VCF file for download: %s" % uuid_vcf) 70 if 'error' in uuid_gff or 'uuid' not in uuid_gff:
63 args.vcf.write(wa.io.download(uuid_vcf['uuid'], output_format="text")) 71 error("Apollo failed to prepare the GFF3 file for download: %s" % uuid_gff)
72 args.gff.write(wa.io.download(uuid_gff['uuid'], output_format="text"))
73 time.sleep(1)
74 except Exception as e:
75 error(e)
64 76
65 time.sleep(1) 77 try:
78 uuid_vcf = wa.io.write_downloadable(org['commonName'], 'VCF', sequences=[sequence['name']])
79 if 'error' in uuid_vcf or 'uuid' not in uuid_vcf:
80 error("Apollo failed to prepare the VCF file for download: %s" % uuid_vcf)
81 args.vcf.write(wa.io.download(uuid_vcf['uuid'], output_format="text"))
82 time.sleep(1)
83 except Exception as e:
84 error(e)
66 85
67 uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=seqs, seq_type='cdna') 86 try:
68 if 'error' in uuid_fa or 'uuid' not in uuid_fa: 87 uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=[sequence['name']], seq_type='cdna')
69 raise Exception("Apollo failed to prepare the cdna FASTA file for download: %s" % uuid_fa) 88 if 'error' in uuid_fa or 'uuid' not in uuid_fa:
70 args.fasta_cdna.write(wa.io.download(uuid_fa['uuid'], output_format="text")) 89 error("Apollo failed to prepare the cdna FASTA file for download: %s" % uuid_fa)
90 args.fasta_cdna.write(wa.io.download(uuid_fa['uuid'], output_format="text"))
91 time.sleep(1)
92 except Exception as e:
93 error(e)
71 94
72 time.sleep(1) 95 try:
96 uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=[sequence['name']], seq_type='cds')
97 if 'error' in uuid_fa or 'uuid' not in uuid_fa:
98 error("Apollo failed to prepare the cds FASTA file for download: %s" % uuid_fa)
99 args.fasta_cds.write(wa.io.download(uuid_fa['uuid'], output_format="text"))
100 time.sleep(1)
101 except Exception as e:
102 error(e)
73 103
74 uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=seqs, seq_type='cds') 104 try:
75 if 'error' in uuid_fa or 'uuid' not in uuid_fa: 105 uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=[sequence['name']], seq_type='peptide')
76 raise Exception("Apollo failed to prepare the cds FASTA file for download: %s" % uuid_fa) 106 if 'error' in uuid_fa or 'uuid' not in uuid_fa:
77 args.fasta_cds.write(wa.io.download(uuid_fa['uuid'], output_format="text")) 107 error("Apollo failed to prepare the file for download: %s" % uuid_fa)
108 args.fasta_pep.write(wa.io.download(uuid_fa['uuid'], output_format="text"))
109 time.sleep(1)
110 except Exception as e:
111 error(e)
78 112
79 time.sleep(1) 113 org_data.append(org)
80
81 uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=seqs, seq_type='peptide')
82 if 'error' in uuid_fa or 'uuid' not in uuid_fa:
83 raise Exception("Apollo failed to prepare the file for download: %s" % uuid_fa)
84 args.fasta_pep.write(wa.io.download(uuid_fa['uuid'], output_format="text"))
85
86 org_data.append(org)
87 114
88 args.json.write(json.dumps(org_data, indent=2)) 115 args.json.write(json.dumps(org_data, indent=2))