8.count-1_depth.py

import string
import sys
from sys import argv

for fn in argv[1:]:
    try:
        f = open(fn)
        msg = "count-1 depth {}".format(fn.strip('./'))
        sys.stdout.write(msg);sys.stdout.flush()
        sys.stdout.write("\b"*len(msg));sys.stdout.flush()
        fnhead = '.'.join(fn.split('.')[:-1])
        fo = open('{}_count-1.txt'.format(fnhead), 'w')
        for line in f.xreadlines():
            units = line.split()
            seq = units[0]
            count = string.atoi(units[1])
            depth = string.atoi(units[2])
            count_1_depth = (count-1)*1.0/depth
            if count-1 != 0 :
                s =  ( seq +" "+ str(count-1) +" "+ str(depth) +" "+ str(count_1_depth*100)+"\n" )
                fo.write(s)

        f.close();fo.close()
        sys.stdout.write(" "*len(msg));sys.stdout.flush()
        sys.stdout.write("\b"*len(msg));sys.stdout.flush()
    except IOError:
        print "IOError"
        pass