INNER CODE UNIT · Python

set_regions

nloyfer/wgbs_tools · src/python/bam2pat.py:49

def set_regions(bam_path, gr, tmp_dir=None):
    # if user specified a region, just use it
    if gr.region_str:
        return [gr.region_str]

    # get all chromosomes from the reference genome:
    ref_chroms = gr.genome.get_chroms()
    if bam_path.endswith('.cram'):
        return list(sorted(ref_chroms, key=chromosome_order))

    # get all chromosomes present in the bam file header
    cmd = f'samtools idxstats {bam_path} | cut -f1 '
    p = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
    output, error = p.communicate()
    if p.returncode or not output:
        eprint("[wt bam2pat] Failed with samtools idxstats %d\n%s\n%s" % (p.returncode, output.decode(), error.decode()))
        eprint(cmd)
        eprint('[wt bam2pat] falied to find chromosomes')

View source record →