Mercurial > repos > gga > apollo_export

comparison export.py @ 13:b763acecfb57 draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 7bf18c69becc57152efdadedf7ebd0bcfa382a15"
author gga
date Mon, 29 Jun 2020 09:11:39 -0400
parents c3b5bc8b4080
children c3251541cf2b
comparison
equal deleted inserted replaced
12:257230cd202f 13:b763acecfb57
50 50
51 org = wa.organisms.show_organism(org_cn) 51 org = wa.organisms.show_organism(org_cn)
52 52
53 uuid_gff = wa.io.write_downloadable(org['commonName'], 'GFF3', export_gff3_fasta=True, sequences=seqs) 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: 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) 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")) 56 args.gff.write(wa.io.download(uuid_gff['uuid'], output_format="text"))
57 57
58 time.sleep(1) 58 time.sleep(1)
59 59
60 uuid_vcf = wa.io.write_downloadable(org['commonName'], 'VCF', sequences=seqs) 60 uuid_vcf = wa.io.write_downloadable(org['commonName'], 'VCF', sequences=seqs)
61 if 'error' in uuid_vcf or 'uuid' not in uuid_vcf: 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) 62 raise Exception("Apollo failed to prepare the VCF file for download: %s" % uuid_vcf)
63 args.vcf.write(wa.io.download(uuid_vcf['uuid'], output_format="text")) 63 args.vcf.write(wa.io.download(uuid_vcf['uuid'], output_format="text"))
64 64
65 time.sleep(1) 65 time.sleep(1)
66 66
67 uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=seqs, seq_type='cdna') 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: 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) 69 raise Exception("Apollo failed to prepare the cdna FASTA file for download: %s" % uuid_fa)
70 args.fasta_cdna.write(wa.io.download(uuid_fa['uuid'], output_format="text")) 70 args.fasta_cdna.write(wa.io.download(uuid_fa['uuid'], output_format="text"))
71 71
72 time.sleep(1) 72 time.sleep(1)
73 73
74 uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=seqs, seq_type='cds') 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: 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) 76 raise Exception("Apollo failed to prepare the cds FASTA file for download: %s" % uuid_fa)
77 args.fasta_cds.write(wa.io.download(uuid_fa['uuid'], output_format="text")) 77 args.fasta_cds.write(wa.io.download(uuid_fa['uuid'], output_format="text"))
78 78
79 time.sleep(1) 79 time.sleep(1)
80 80
81 uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=seqs, seq_type='peptide') 81 uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=seqs, seq_type='peptide')