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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Contra/scripts/split_chromosome.py	Thu Sep 13 02:31:43 2012 -0400
@@ -0,0 +1,105 @@
+# ----------------------------------------------------------------------#
+# 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()
+
+