INNER CODE UNIT · Python

gen_pat_part

nloyfer/wgbs_tools · src/python/bam2pat.py:88

def gen_pat_part(out_path, debug, temp_dir, long):
    try:
        # if out_path is empty or missing, return None
        if not op.isfile(out_path):
            eprint(f'[wt bam2pat] Failed in patter: file {out_path} is missing')
            return
        if op.getsize(out_path) == 0:
            eprint(f'[wt bam2pat] Failed in patter: file {out_path} is empty')
            return
        # sort
        pat_path = out_path + PAT_SUFF
        cmd = f'sort {out_path} -k2,2n -k3,3 '
        if temp_dir:
            cmd += f' -T {temp_dir} '
        if long:
            cmd += " | awk -v OFS='\t' '{print $1,$2,$3,1,$4}'"
        else:
            cmd += " | uniq -c | awk -v OFS='\t' '{print $2,$3,$4,$1}'"

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