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')
