gff_to_embl.py

#!/usr/bin/env python
"""Convert a GFF and associated FASTA file into GenBank format.
Usage:
    gff_to_genbank.py <GFF annotation file> <FASTA sequence file>
"""
import sys
import os

from Bio import SeqIO
from Bio.Alphabet import generic_dna
from Bio import Seq

from BCBio import GFF

def main(gff_file, fasta_file, output_directory):
    if not os.path.exists(output_directory):
        os.makedirs(output_directory)
    print("Loading FASTA")
    fasta_input = SeqIO.to_dict(SeqIO.parse(fasta_file, "fasta", generic_dna))
    print("Loading GFF")
    gff_iter = GFF.parse(gff_file, fasta_input)
    print("Writing EMBL")
    for seq in _check_gff(_fix_ncbi_id(gff_iter)):
        SeqIO.write(seq, "{}/{}.embl".format(output_directory, seq.name), "embl")

def _fix_ncbi_id(fasta_iter):
    """GenBank identifiers can only be 16 characters; try to shorten NCBI.
    """
    for rec in fasta_iter:
        if len(rec.name) > 16 and rec.name.find("|") > 0:
            new_id = [x for x in rec.name.split("|") if x][-1]
            print "Warning: shortening NCBI name %s to %s" % (rec.id, new_id)
            rec.id = new_id
            rec.name = new_id
        yield rec

def _check_gff(gff_iterator):
    """Check GFF files before feeding to SeqIO to be sure they have sequences.
    """
    for rec in gff_iterator:
        if isinstance(rec.seq, Seq.UnknownSeq):
            print "Warning: FASTA sequence not found for '%s' in GFF file" % (
                    rec.id)
            rec.seq.alphabet = generic_dna
        yield _flatten_features(rec)

def _flatten_features(rec):
    """Make sub_features in an input rec flat for output.
    GenBank does not handle nested features, so we want to make
    everything top level.
    """
    out = []
    for f in rec.features:
        cur = [f]
        while len(cur) > 0:
            nextf = []
            for curf in cur:
                out.append(curf)
                if len(curf.sub_features) > 0:
                    nextf.extend(curf.sub_features)
            cur = nextf
    rec.features = out
    return rec

if __name__ == "__main__":
    main(*sys.argv[1:])