#!/usr/bin/env python
"""
Usage is:

bamerrors_cutoff.py -c cutoff list_of_bamerrors_output_files

Writes output to bamerrors_cutoff.txt in the current directory.
Output identifies columns that are >= cutoff.  Format is the 
following 4 columns: filename, rowID,  columnID, value


"""

import sys
import os
import getopt
import subprocess
import re
from decimal import *



def main(argv=None):
    if argv is None:
        argv=sys.argv

    outputFilename = "bamerrors_cutoff.txt"
    cutoff = None
    options, errfiles= getopt.getopt(argv[1:], "c:")
    for opt, arg in options:
        if opt in ("-c"):
            cutoff = Decimal(arg)
    if (not cutoff):
        print >> sys.stderr, __doc__
        return
    findHighErrors(outputFilename, cutoff, errfiles)    

    

def findHighErrors(outputFilename, cutoff, errFiles):

    outfile = open(outputFilename, "w")

    for filename in errFiles:
        fp = open(filename, "r")
        fp.readline() # skip the header
        while True:
            line = fp.readline()
            if not line:
                break
            fields = line.split()
            rowname = fields[0]
            for col in range(1, len(fields) - 1):
                if Decimal(fields[col]) >= cutoff:
                    outfile.write("%s\t%s\t%d\t%s\n" % ( filename, rowname, col, fields[col]))
        fp.close()
        outfile.flush()

    outfile.close()
    
    

if __name__ == "__main__":
    sys.exit(main())