extract_gene_seq.py 文件源码

def main(opts):
    # read bed file, extract gene sequence from genome, write to fasta
    genome_fa = pysam.Fastafile(opts['input'])
    with open(opts['output'], 'w') as handle:
        for bed_row in utils.bed_generator(opts['bed']):
            fasta_seq = gs.fetch_gene_fasta(bed_row, genome_fa)
            handle.write(fasta_seq)
    genome_fa.close()