def main( gff_file, fasta_file, outfile, oformat ): fasta_input = SeqIO.to_dict(SeqIO.parse(fasta_file, "fasta", generic_dna)) gff_iter = GFF.parse(gff_file, fasta_input) gff_iter = add_translation(gff_iter) if oformat in ['genbank', 'gb']: SeqIO.write(check_gff(fix_ncbi_id(gff_iter)), outfile, oformat) else: SeqIO.write(check_gff(gff_iter), outfile, oformat)
def main(gff_file, fasta_file, outfile, oformat): fasta_input = SeqIO.to_dict(SeqIO.parse(fasta_file, "fasta", generic_dna)) gff_iter = GFF.parse(gff_file, fasta_input) #gff_iter = add_translation(gff_iter) if oformat in ['genbank', 'gb']: SeqIO.write(check_gff(fix_ncbi_id(gff_iter)), outfile, oformat) else: SeqIO.write(check_gff(gff_iter), outfile, oformat)
def main(gff_file, ref_file, ofile, seq_type="CDS"): with open(ref_file) as in_handle: fasta_recs = SeqIO.to_dict(SeqIO.parse(in_handle, "fasta")) base, ext = os.path.splitext(gff_file) gff_iter = GFF.parse(gff_file, fasta_recs) recs = protein_recs(check_gff(gff_iter), fasta_recs, seq_type) SeqIO.write(recs, ofile, "fasta")
def main(gff_file, ref_file, ofile, seq_type='CDS'): with open(ref_file) as in_handle: fasta_recs = SeqIO.to_dict(SeqIO.parse(in_handle, "fasta")) base, ext = os.path.splitext(gff_file) gff_iter = GFF.parse(gff_file, fasta_recs) recs = protein_recs(check_gff(gff_iter), fasta_recs, seq_type) SeqIO.write(recs, ofile, 'fasta')