chrosome sizes

gistfile1.txt

#!/usr/bin/env python

import os
import sys

if len(sys.argv) != 2:
    print "Usage %s: samtools_index" % os.path.basename(sys.argv[0])
    sys.exit(1)

samtools_index = sys.argv[1]

with open(samtools_index) as f:
    prev_chrom = None
    prev_size = 0
        
    for line in f:
        cols = line.split('\t')
        chrom = cols[0]
        chrom_size = int(cols[1])
        
        if chrom[-1].isdigit():
            if prev_size:
                length_diff = prev_size - chrom_size
                if length_diff < 0:
                    print "%s longer than %s by %d bases!" % (chrom, prev_chrom, -length_diff)
            prev_chrom = chrom
            prev_size = chrom_size