Mercurial > repos > gga > apollo_feat_from_gff3

comparison export.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 bb562d95b6cd
comparison
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9:09dacc7c6a21 10:5d1cf95ade8a
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 from __future__ import print_function 2 from __future__ import print_function
3 3
4 import argparse 4 import argparse
5 import json 5 import json
6 import sys 6 import time
7 7
8 from BCBio import GFF 8 from apollo import accessible_organisms
9 from apollo.util import CnOrGuess, GuessCn
9 10
10 from Bio import SeqIO 11 from arrow.apollo import get_apollo_instance
11 12
12 from webapollo import CnOrGuess, GuessCn, PermissionCheck, WAAuth, WebApolloInstance 13 from webapollo import UserObj, handle_credentials
13
14 try:
15 import StringIO as io
16 except ImportError:
17 import io
18
19
20 def export(org_cn, seqs):
21 org_data = wa.organisms.findOrganismByCn(org_cn)
22
23 data = io.StringIO()
24
25 kwargs = dict(
26 exportType='GFF3',
27 seqType='genomic',
28 exportGff3Fasta=True,
29 output="text",
30 exportFormat="text",
31 organism=org_cn,
32 )
33
34 if len(seqs) > 0:
35 data.write(wa.io.write(
36 exportAllSequences=False,
37 sequences=seqs,
38 **kwargs
39 ).encode('utf-8'))
40 else:
41 data.write(wa.io.write(
42 exportAllSequences=True,
43 sequences=[],
44 **kwargs
45 ).encode('utf-8'))
46
47 # Seek back to start
48 data.seek(0)
49
50 records = list(GFF.parse(data))
51 if len(records) == 0:
52 print("Could not find any sequences or annotations for this organism + reference sequence")
53 sys.exit(2)
54 else:
55 for record in records:
56 record.annotations = {}
57 record.features = sorted(record.features, key=lambda x: x.location.start)
58 if args.gff:
59 GFF.write([record], args.gff)
60 record.description = ""
61 if args.fasta:
62 SeqIO.write([record], args.fasta, 'fasta')
63
64 return org_data
65
66 14
67 if __name__ == '__main__': 15 if __name__ == '__main__':
68 parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services') 16 parser = argparse.ArgumentParser(description='Script to export data from Apollo via web services')
69 WAAuth(parser)
70 CnOrGuess(parser) 17 CnOrGuess(parser)
71 parser.add_argument('--gff', type=argparse.FileType('w')) 18 parser.add_argument('--gff', type=argparse.FileType('w'))
72 parser.add_argument('--fasta', type=argparse.FileType('w')) 19 parser.add_argument('--fasta_pep', type=argparse.FileType('w'))
20 parser.add_argument('--fasta_cds', type=argparse.FileType('w'))
21 parser.add_argument('--fasta_cdna', type=argparse.FileType('w'))
22 parser.add_argument('--vcf', type=argparse.FileType('w'))
73 parser.add_argument('--json', type=argparse.FileType('w')) 23 parser.add_argument('--json', type=argparse.FileType('w'))
74 parser.add_argument('email', help='User Email') 24 parser.add_argument('email', help='User Email')
75 args = parser.parse_args() 25 args = parser.parse_args()
76 26
77 wa = WebApolloInstance(args.apollo, args.username, args.password) 27 wa = get_apollo_instance()
78
79 org_cn_list, seqs = GuessCn(args, wa)
80 28
81 # User must have an apollo account, if not, create it 29 # User must have an apollo account, if not, create it
82 gx_user = wa.users.assertOrCreateUser(args.email) 30 gx_user = UserObj(**wa.users._assert_or_create_user(args.email))
31 handle_credentials(gx_user)
32
33 org_cns, seqs = GuessCn(args, wa)
34 if not isinstance(org_cns, list):
35 org_cns = [org_cns]
36
37 all_orgs = wa.organisms.get_organisms()
38 if 'error' in all_orgs:
39 all_orgs = []
40 all_orgs = [org['commonName'] for org in all_orgs]
83 41
84 org_data = [] 42 org_data = []
85 for org_cn in org_cn_list: 43 for org_cn in org_cns:
86 # User must have read permission on organism 44 if org_cn not in all_orgs:
87 if not PermissionCheck(gx_user, org_cn, "READ"): 45 raise Exception("Could not find organism %s" % org_cn)
88 continue 46
89 indiv_org_data = export(org_cn, seqs) 47 orgs = accessible_organisms(gx_user, [org_cn], 'READ')
90 org_data.append(indiv_org_data) 48 if not orgs:
49 raise Exception("You do not have read permission on organism %s" % org_cn)
50
51 org = wa.organisms.show_organism(org_cn)
52
53 uuid_gff = wa.io.write_downloadable(org['commonName'], 'GFF3', export_gff3_fasta=True, sequences=seqs)
54 if 'error' in uuid_gff or 'uuid' not in uuid_gff:
55 raise Exception("Apollo failed to prepare the file for download: %s" % uuid_gff)
56 args.gff.write(wa.io.download(uuid_gff['uuid'], output_format="text"))
57
58 time.sleep(1)
59
60 uuid_vcf = wa.io.write_downloadable(org['commonName'], 'VCF', sequences=seqs)
61 if 'error' in uuid_vcf or 'uuid' not in uuid_vcf:
62 raise Exception("Apollo failed to prepare the file for download: %s" % uuid_vcf)
63 args.vcf.write(wa.io.download(uuid_vcf['uuid'], output_format="text"))
64
65 time.sleep(1)
66
67 uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=seqs, seq_type='cdna')
68 if 'error' in uuid_fa or 'uuid' not in uuid_fa:
69 raise Exception("Apollo failed to prepare the file for download: %s" % uuid_fa)
70 args.fasta_cdna.write(wa.io.download(uuid_fa['uuid'], output_format="text"))
71
72 time.sleep(1)
73
74 uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=seqs, seq_type='cds')
75 if 'error' in uuid_fa or 'uuid' not in uuid_fa:
76 raise Exception("Apollo failed to prepare the file for download: %s" % uuid_fa)
77 args.fasta_cds.write(wa.io.download(uuid_fa['uuid'], output_format="text"))
78
79 time.sleep(1)
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
91 args.json.write(json.dumps(org_data, indent=2)) 88 args.json.write(json.dumps(org_data, indent=2))