Mercurial > repos > gga > apollo_feat_from_gff3

annotate export.py @ 14:9f9aa5a88972 draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 7f274d9deece87f6837ffb0a22d9231671be4542"
author gga
date Wed, 19 Aug 2020 06:54:11 -0400
parents bb562d95b6cd
children 12ebb583b8a3
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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
5aa3bc8d0253 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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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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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('--fasta_pep', type=argparse.FileType('w'))
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20 parser.add_argument('--fasta_cds', type=argparse.FileType('w'))
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21 parser.add_argument('--fasta_cdna', type=argparse.FileType('w'))
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22 parser.add_argument('--vcf', type=argparse.FileType('w'))
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23 parser.add_argument('--json', type=argparse.FileType('w'))
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24 parser.add_argument('email', help='User Email')
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25 args = parser.parse_args()
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27 wa = get_apollo_instance()
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29 # User must have an apollo account, if not, create it
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30 gx_user = UserObj(**wa.users._assert_or_create_user(args.email))
5d1cf95ade8a "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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31 handle_credentials(gx_user)
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33 org_cns, seqs = GuessCn(args, wa)
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34 if not isinstance(org_cns, list):
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35 org_cns = [org_cns]
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37 all_orgs = wa.organisms.get_organisms()
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38 if 'error' in all_orgs:
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39 all_orgs = []
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40 all_orgs = [org['commonName'] for org in all_orgs]
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42 org_data = []
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43 for org_cn in org_cns:
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44 if org_cn not in all_orgs:
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45 raise Exception("Could not find organism %s" % org_cn)
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47 orgs = accessible_organisms(gx_user, [org_cn], 'READ')
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48 if not orgs:
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49 raise Exception("You do not have read permission on organism %s" % org_cn)
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51 org = wa.organisms.show_organism(org_cn)
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53 uuid_gff = wa.io.write_downloadable(org['commonName'], 'GFF3', export_gff3_fasta=True, sequences=seqs)
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54 if 'error' in uuid_gff or 'uuid' not in uuid_gff:
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55 raise Exception("Apollo failed to prepare the GFF3 file for download: %s" % uuid_gff)
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56 args.gff.write(wa.io.download(uuid_gff['uuid'], output_format="text"))
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58 time.sleep(1)
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60 uuid_vcf = wa.io.write_downloadable(org['commonName'], 'VCF', sequences=seqs)
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61 if 'error' in uuid_vcf or 'uuid' not in uuid_vcf:
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62 raise Exception("Apollo failed to prepare the VCF file for download: %s" % uuid_vcf)
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63 args.vcf.write(wa.io.download(uuid_vcf['uuid'], output_format="text"))
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65 time.sleep(1)
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67 uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=seqs, seq_type='cdna')
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68 if 'error' in uuid_fa or 'uuid' not in uuid_fa:
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69 raise Exception("Apollo failed to prepare the cdna FASTA file for download: %s" % uuid_fa)
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70 args.fasta_cdna.write(wa.io.download(uuid_fa['uuid'], output_format="text"))
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72 time.sleep(1)
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74 uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=seqs, seq_type='cds')
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75 if 'error' in uuid_fa or 'uuid' not in uuid_fa:
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76 raise Exception("Apollo failed to prepare the cds FASTA file for download: %s" % uuid_fa)
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77 args.fasta_cds.write(wa.io.download(uuid_fa['uuid'], output_format="text"))
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79 time.sleep(1)
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81 uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=seqs, seq_type='peptide')
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82 if 'error' in uuid_fa or 'uuid' not in uuid_fa:
5d1cf95ade8a "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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83 raise Exception("Apollo failed to prepare the file for download: %s" % uuid_fa)
5d1cf95ade8a "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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84 args.fasta_pep.write(wa.io.download(uuid_fa['uuid'], output_format="text"))
5d1cf95ade8a "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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85
5d1cf95ade8a "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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86 org_data.append(org)
5d1cf95ade8a "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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87
0
5aa3bc8d0253 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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88 args.json.write(json.dumps(org_data, indent=2))