Get contig information by `samtools view -H`

get_contigs.py

def get_contigs(bam_path):
    """Get contig information by `samtools view -H`

    Arg:
    bam_path: path to a bam-file

    RetVal:
    ['chr1', 'chr2', ..., 'chrM']
    """

    contigs = []

    com = ['samtools', 'view', '-H', bam_path]
    proc =  subprocess.Popen(com, stdout=subprocess.PIPE)

    while True:
      line = proc.stdout.readline()
      if not line:
          break

      record = line.split('\t')
      if record[0] == '@SQ':
          chrom = record[1].replace('SN:', '')
          contigs.append(chrom)

    return contigs