Count mapped reads and unmapped reads in bam files.

count-bam.py

#!/usr/bin/env python

import argparse
import pysam

def _main():
    parser = argparse.ArgumentParser(description="Count mapped reads and unmapped reads")
    parser.add_argument('bam', nargs='+')
    options = parser.parse_args()

    print '\t'.join(['file', 'mapped', 'unmapped', 'total'])
    for one in options.bam:
        onefile = pysam.Samfile(one, 'rb')
        print '\t'.join([str(x) for x in [one, onefile.mapped, onefile.unmapped, onefile.mapped+onefile.unmapped]])
    
    
if __name__ == '__main__':
    _main()