Mercurial > repos > eric-rasche > apollo
view export.py @ 0:6002cc0df04e draft
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
author | eric-rasche |
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date | Tue, 03 May 2016 13:38:55 -0400 |
parents | |
children | d4ae83dedb14 |
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#!/usr/bin/env python import StringIO import sys import json import argparse from Bio import SeqIO from BCBio import GFF from webapollo import WebApolloInstance if __name__ == '__main__': json parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services') parser.add_argument('apollo', help='Complete Apollo URL') parser.add_argument('username', help='WA Username') parser.add_argument('password', help='WA Password') parser.add_argument('commonName', nargs='+', help='Sequence Unique Names') parser.add_argument('--gff', type=argparse.FileType('w')) parser.add_argument('--fasta', type=argparse.FileType('w')) args = parser.parse_args() wa = WebApolloInstance(args.apollo, args.username, args.password) data = StringIO.StringIO(wa.io.write( exportType='GFF3', seqType='genomic', exportAllSequences=False, exportGff3Fasta=True, output="text", exportFormat="text", # TODO: CPT specific convention!!!!!!!! organism=args.commonName, sequences=args.commonName )) data.seek(0) for record in GFF.parse(data): record.annotations = {} GFF.write([record], args.gff) record.description = "" SeqIO.write([record], args.fasta, 'fasta') sys.exit()