Mercurial > repos > gga > apollo_list_organism
view export.py @ 0:1f2e360f7554 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
author | gga |
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date | Mon, 11 Sep 2017 05:48:05 -0400 |
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children | b69804a685e2 |
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#!/usr/bin/env python from __future__ import print_function import argparse import json import sys from BCBio import GFF from Bio import SeqIO from future import standard_library from webapollo import CnOrGuess, GuessCn, WAAuth, WebApolloInstance standard_library.install_aliases() try: import StringIO as io except ImportError: import io def export(org_cn, seqs): org_data = wa.organisms.findOrganismByCn(org_cn) data = io.StringIO() kwargs = dict( exportType='GFF3', seqType='genomic', exportGff3Fasta=True, output="text", exportFormat="text", organism=org_cn, ) if len(seqs) > 0: data.write(wa.io.write( exportAllSequences=False, sequences=seqs, **kwargs ).encode('utf-8')) else: data.write(wa.io.write( exportAllSequences=True, sequences=[], **kwargs ).encode('utf-8')) # Seek back to start data.seek(0) records = list(GFF.parse(data)) if len(records) == 0: print("Could not find any sequences or annotations for this organism + reference sequence") sys.exit(2) else: for record in records: record.annotations = {} record.features = sorted(record.features, key=lambda x: x.location.start) if args.gff: GFF.write([record], args.gff) record.description = "" if args.fasta: SeqIO.write([record], args.fasta, 'fasta') return org_data if __name__ == '__main__': parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services') WAAuth(parser) CnOrGuess(parser) parser.add_argument('--gff', type=argparse.FileType('w')) parser.add_argument('--fasta', type=argparse.FileType('w')) parser.add_argument('--json', type=argparse.FileType('w')) args = parser.parse_args() wa = WebApolloInstance(args.apollo, args.username, args.password) org_cn_list, seqs = GuessCn(args, wa) org_data = [] for org_cn in org_cn_list: indiv_org_data = export(org_cn, seqs) org_data.append(indiv_org_data) args.json.write(json.dumps(org_data, indent=2))