Pretty simple CLI tool for generating fasta record from genomic region defined by GFF record

tofa.py

from pyfasta import Fasta
import HTSeq
import argparse
import re

def __mk_rna(*seq):
    return re.sub(r"[tT]", "U", "".join(seq)).upper()

def __query_builder(rec):
    if not isinstance(rec, HTSeq.GenomicFeature):
        raise TypeError()
    else:
        return {"chr": rec.iv.chrom, "start": rec.iv.start, "stop": rec.iv.end, "strand": rec .iv.strand}

def __extract_sequence(q, genome):
    fa = Fasta(genome)
    return fa.sequence(q)

def __to_fasta(header, seq):
    return ">%s\n%s" % (header, seq)

def GFF_to_Fasta(args):
    for rec in HTSeq.GFF_Reader(args.gff):
        query = __query_builder(rec)
        seq = __extract_sequence(query, args.genome)
        header = rec.attr["Name"] + ":" + rec.attr["transcript_id"]
        print __to_fasta(header, __mk_rna(seq))

if __name__ == "__main__":
    parse = argparse.ArgumentParser(description="Generate fasta sequence from GFF record")
    parse.add_argument("--genome", type=str, dest="genome", help="Genome sequence", required=True)
    parse.add_argument("--gff", type=str, dest="gff", help="GFF file", required=True)
    args = parse.parse_args()
    GFF_to_Fasta(args)