Python definitions to take genbank file containing multiple genomes and dividing them into fasta protein files, one file per genome. For Stackoverflow question http://stackoverflow.com/posts/34777323/

gbk_to_faa.py

from operator import itemgetter
from itertools import groupby

def gbk_to_faa(some_genbank):
    source = None
    for record in SeqIO.parse(some_genbank, 'gb'):
        if source:
            if record.annotations['source'] != source:
                out_file.close()
                source = sub(r'\W+', "_", sub(r'\W$', "", record.annotations['source']))
                out_file = open("{}.faa".format(source), "a+")
                write_all_record(out_file, record)
            else:
                write_all_record(out_file, record)
        else:
            source = sub(r'\W+', "_", sub(r'\W$', "", record.annotations['source']))
            out_file = open("{}.faa".format(source), "a+")
            write_all_record(out_file, record)

    out_file.close()


def write_all_record(file_handle, gbk_record):
    for feature in gbk_record.features:
                    if feature.type == "CDS":
                        tag = feature.qualifiers['locus_tag'][0]
                        seq = feature.qualifiers['translation'][0]
                        fasta(file_handle, tag, seq)


def fasta(file_handle, id, seq):
    file_handle.write(">{}\n{}\n".format(id, seq))
    
def from_stack(some_genbank):
    for name, records in groupby(SeqIO.parse(some_genbank, 'gb'), lambda record:record.annotations['source']):
        with open(name + ".faa", "w+") as outf:
            for record in records:
                write_all_record(outf, record)