mapping_stats.py - for BLASR SAM output, requires Pysam

mapping_stats.py

import pysam
import sys

samfile = pysam.Samfile(sys.argv[1], "rb")

fields = ['Name', 'QueryLen', 'AlignLen', 'NumMismatches']
print "\t".join(fields)

for read in samfile:
        t = dict(read.tags)

        results = []
        results.append(read.qname.ljust(25))
        results.append(t['XQ'])
        results.append(t['XL'])
        results.append(t['NM'])

        print "\t".join([str(r) for r in results])