Mercurial > repos > vipints > fml_gff3togtf
view gff_to_gbk.py @ 7:ee541c1852da
Uploaded version 2.1.0
author | vipints |
---|---|
date | Thu, 23 Apr 2015 17:43:11 -0400 |
parents | 6e589f267c14 |
children |
line wrap: on
line source
#!/usr/bin/env python """ Convert data from GFF and associated genome sequence in fasta file into GenBank. Usage: python gff_to_gbk.py in.gff in.fasta out.gbk Requirements: BioPython:- http://biopython.org/ helper.py : https://github.com/vipints/GFFtools-GX/blob/master/helper.py Copyright (C) 2010-2012 Friedrich Miescher Laboratory of the Max Planck Society, Tubingen, Germany. 2012-2014 Memorial Sloan Kettering Cancer Center New York City, USA. """ import sys import helper import gffparser_bcbio from Bio import SeqIO from Bio.Alphabet import generic_dna def __main__(): """ main wrapper """ try: gff_fname = sys.argv[1] fasta_fname = sys.argv[2] gb_fname = sys.argv[3] except: print __doc__ sys.exit(-1) fasta_fh = helper.open_file(fasta_fname) fasta_rec = SeqIO.to_dict(SeqIO.parse(fasta_fh, "fasta", generic_dna)) fasta_fh.close() gff_rec = gffparser_bcbio.parse(gff_fname, fasta_rec) try: gb_fh = open(gb_fname, "w") except: print 'file not ready for writing %s' % gb_fname sys.exit(-1) SeqIO.write(gff_rec, gb_fh, "genbank") gb_fh.close() if __name__=="__main__": __main__()