Mercurial > repos > gga > apollo_feat_from_gff3

annotate 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
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5aa3bc8d0253 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 json
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6 import time
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8 from apollo import accessible_organisms
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9 from apollo.util import CnOrGuess, GuessCn
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11 from arrow.apollo import get_apollo_instance
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13 from webapollo import UserObj, handle_credentials
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5aa3bc8d0253 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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15 if __name__ == '__main__':
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16 parser = argparse.ArgumentParser(description='Script to export data from Apollo via web services')
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17 CnOrGuess(parser)
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18 parser.add_argument('--gff', type=argparse.FileType('w'))
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19 parser.add_argument('--gff_with_fasta', action='store_true')
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20 parser.add_argument('--fasta_pep', type=argparse.FileType('w'))
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21 parser.add_argument('--fasta_cds', type=argparse.FileType('w'))
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22 parser.add_argument('--fasta_cdna', type=argparse.FileType('w'))
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23 parser.add_argument('--vcf', type=argparse.FileType('w'))
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24 parser.add_argument('--json', type=argparse.FileType('w'))
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25 parser.add_argument('--die', action='store_true')
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26 parser.add_argument('email', help='User Email')
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27 args = parser.parse_args()
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29 wa = get_apollo_instance()
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31 # User must have an apollo account, if not, create it
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32 gx_user = UserObj(**wa.users._assert_or_create_user(args.email))
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33 handle_credentials(gx_user)
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35 org_cns, seqs = GuessCn(args, wa)
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36 if not isinstance(org_cns, list):
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37 org_cns = [org_cns]
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39 all_orgs = wa.organisms.get_organisms()
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40 if 'error' in all_orgs:
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41 all_orgs = []
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42 all_orgs = [org['commonName'] for org in all_orgs]
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44 def error(message):
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45 if args.die:
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46 raise Exception(message)
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47 else:
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48 print(message)
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49
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50 org_data = []
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51 for org_cn in org_cns:
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52 if org_cn not in all_orgs:
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53 raise Exception("Could not find organism %s" % org_cn)
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54
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55 orgs = accessible_organisms(gx_user, [org_cn], 'READ')
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56 if not orgs:
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57 raise Exception("You do not have read permission on organism %s" % org_cn)
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59 org = wa.organisms.show_organism(org_cn)
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61 # Fetch all the refseqs
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62 realSeqs = wa.organisms.get_sequences(org['id'])
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64 # We'll loop over them individually for decreased memory pressure
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65 for sequence in realSeqs['sequences']:
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66 print("Downloading", sequence)
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67
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68 try:
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69 uuid_gff = wa.io.write_downloadable(org['commonName'], 'GFF3', export_gff3_fasta=args.gff_with_fasta, sequences=[sequence['name']])
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70 if 'error' in uuid_gff or 'uuid' not in uuid_gff:
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71 error("Apollo failed to prepare the GFF3 file for download: %s" % uuid_gff)
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72 args.gff.write(wa.io.download(uuid_gff['uuid'], output_format="text"))
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73 time.sleep(1)
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74 except Exception as e:
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75 error(e)
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76
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77 try:
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78 uuid_vcf = wa.io.write_downloadable(org['commonName'], 'VCF', sequences=[sequence['name']])
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79 if 'error' in uuid_vcf or 'uuid' not in uuid_vcf:
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80 error("Apollo failed to prepare the VCF file for download: %s" % uuid_vcf)
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81 args.vcf.write(wa.io.download(uuid_vcf['uuid'], output_format="text"))
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82 time.sleep(1)
12ebb583b8a3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
gga
parents: 13
diff changeset
83 except Exception as e:
12ebb583b8a3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
gga
parents: 13
diff changeset
84 error(e)
10
5d1cf95ade8a "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
85
16
12ebb583b8a3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
gga
parents: 13
diff changeset
86 try:
12ebb583b8a3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
gga
parents: 13
diff changeset
87 uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=[sequence['name']], seq_type='cdna')
12ebb583b8a3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
gga
parents: 13
diff changeset
88 if 'error' in uuid_fa or 'uuid' not in uuid_fa:
12ebb583b8a3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
gga
parents: 13
diff changeset
89 error("Apollo failed to prepare the cdna FASTA file for download: %s" % uuid_fa)
12ebb583b8a3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
gga
parents: 13
diff changeset
90 args.fasta_cdna.write(wa.io.download(uuid_fa['uuid'], output_format="text"))
12ebb583b8a3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
gga
parents: 13
diff changeset
91 time.sleep(1)
12ebb583b8a3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
gga
parents: 13
diff changeset
92 except Exception as e:
12ebb583b8a3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
gga
parents: 13
diff changeset
93 error(e)
10
5d1cf95ade8a "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
94
16
12ebb583b8a3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
gga
parents: 13
diff changeset
95 try:
12ebb583b8a3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
gga
parents: 13
diff changeset
96 uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=[sequence['name']], seq_type='cds')
12ebb583b8a3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
gga
parents: 13
diff changeset
97 if 'error' in uuid_fa or 'uuid' not in uuid_fa:
12ebb583b8a3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
gga
parents: 13
diff changeset
98 error("Apollo failed to prepare the cds FASTA file for download: %s" % uuid_fa)
12ebb583b8a3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
gga
parents: 13
diff changeset
99 args.fasta_cds.write(wa.io.download(uuid_fa['uuid'], output_format="text"))
12ebb583b8a3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
gga
parents: 13
diff changeset
100 time.sleep(1)
12ebb583b8a3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
gga
parents: 13
diff changeset
101 except Exception as e:
12ebb583b8a3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
gga
parents: 13
diff changeset
102 error(e)
10
5d1cf95ade8a "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
103
16
12ebb583b8a3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
gga
parents: 13
diff changeset
104 try:
12ebb583b8a3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
gga
parents: 13
diff changeset
105 uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=[sequence['name']], seq_type='peptide')
12ebb583b8a3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
gga
parents: 13
diff changeset
106 if 'error' in uuid_fa or 'uuid' not in uuid_fa:
12ebb583b8a3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
gga
parents: 13
diff changeset
107 error("Apollo failed to prepare the file for download: %s" % uuid_fa)
12ebb583b8a3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
gga
parents: 13
diff changeset
108 args.fasta_pep.write(wa.io.download(uuid_fa['uuid'], output_format="text"))
12ebb583b8a3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
gga
parents: 13
diff changeset
109 time.sleep(1)
12ebb583b8a3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
gga
parents: 13
diff changeset
110 except Exception as e:
12ebb583b8a3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
gga
parents: 13
diff changeset
111 error(e)
10
5d1cf95ade8a "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
112
16
12ebb583b8a3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
gga
parents: 13
diff changeset
113 org_data.append(org)
10
5d1cf95ade8a "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
114
0
5aa3bc8d0253 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
115 args.json.write(json.dumps(org_data, indent=2))