comparison Contra/scripts/split_chromosome.py @ 0:7564f3b1e675

Uploaded

0:7564f3b1e675

# ----------------------------------------------------------------------#
# Copyright (c) 2011, Richard Lupat & Jason Li.
#
# > Source License <
# This file is part of CONTRA.
#
#    CONTRA is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    CONTRA is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details.
#
#    You should have received a copy of the GNU General Public License
#    along with CONTRA.  If not, see <http://www.gnu.org/licenses/>.
#
# 
#-----------------------------------------------------------------------#
# Last Updated : 03 Sep 2011 15:00PM


import os

def splitByChromosome(destFolder):

	try:
		os.mkdir(destFolder + "chr/")
	except:
		print "folder exist"

	inputfile = destFolder + "sample.BEDGRAPH"
	outputfile = destFolder + "chr/chr1.txt"
	file = open(inputfile,"r")
	output = open(outputfile,"w")
	check = "1"

	for row in file:
		if row[0] == '#':
			continue

		cols = row.split()
		chr = cols[0].strip("chr")
		if (chr != check):
			output.close()
			check = chr
			output = open(destFolder+ "chr/chr"+check+".txt","w")
		output.write(row)

	output.close()

#JLMod
def splitByChromosome3(infile):
        destFolder = os.path.dirname(infile)+"/"

        try:
                os.mkdir(destFolder + "chr/")
        except:
                print "folder exist"

        #inputfile = destFolder + "sample.BEDGRAPH"
        inputfile=infile
        outputfile = destFolder + "chr/chr1.txt"
        file = open(inputfile,"r")
        output = open(outputfile,"w")
        check = "1"

        for row in file:
                cols = row.split()
                chr = cols[0].strip("chr")
                if (chr != check):
                        output.close()
                        check = chr
                        output = open(destFolder+ "chr/chr"+check+".txt","w")
                output.write(row)

        output.close()

def splitByChromosome2(folder):

        try:
                os.mkdir(folder + "target/")
        except:
                print "folder exist"

        inputfile = folder + "geneRefCoverage.txt"
        outputfile = folder + "target/chr1.txt"
        file = open(inputfile,"r")
        output = open(outputfile,"w")
        check = "1"

        for row in file:
                cols = row.split()
                chr = cols[0].strip("chr")
                if (chr != check):
                        output.close()
                        check = chr
                        output = open(folder+ "target/chr"+check+".txt","w")
                output.write(row)

        output.close()