view Contra/scripts/cn_apply_threshold.py @ 11:b6ce842a633d

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# ----------------------------------------------------------------------#
# 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 : 12 Oct 2011 11:00AM

def applyThreshold(outputName, bufTable, threshold, maxGap):
	srcFile = outputName + ".txt"
	outFile = bufTable + ".LargeVariations.txt"
	bedFile = bufTable + ".BED"
	fFile 	= outputName + ".DetailsFILTERED.txt" 
	ts	= float(threshold)

	# Read and open files
	srcTable = file.readlines(open(srcFile))
	outTable = open(outFile, "w")
	bedOut	 = open(bedFile, "w")
	filteredTable = open(fFile, "w")


	#header
	outTable.write("Chr \tStartCoordinate \tEndCoordinate \tGenes \tGain.Loss \n")
	filteredTable.write(srcTable[0])

	prevChr = ''
	prevStatus = ''
	prevEnd = -1
	genes = []
	chrList = []

	for exons in srcTable:
		exon = exons.split()
		try:
			adjPVal = float(exon[12])
		except:
			continue

		if adjPVal <= ts:
			chr 	= exon[3]
			gene 	= exon[2]
			status 	= exon[13]
			start 	= exon[4]
			end	= exon[5]

			# For first row
			if prevEnd == -1:
				gap = 0
			else:
				gap = int(prevEnd) - int(start)

			# Write Filtered Table
			filteredTable.write(exons)

			# Write Bed File
			bedOut.write(chr.strip("chr") +"\t" +start +"\t"+ end+"\t"+ 
			   chr.strip("chr")+":"+start+"-"+end+":"+str(adjPVal)+"\n")
		
			if prevChr == '' and prevStatus == '':
				if chr not in chrList:
					print chr
					chrList.append(chr)
			elif (chr == prevChr) and (status == prevStatus) and (gap < maxGap):
				start = prevStart
			else:
				outTable.write(prevChr +"\t" +prevStart +"\t" +prevEnd + "\t")
				for gsym in genes:
					outTable.write(gsym + ", ")
				outTable.write("\t" + prevStatus + "\n")
				genes=[]
		
			if gene not in genes:
				genes.append(gene)
			prevChr = chr
			prevStatus = status
			prevStart = start
			prevEnd = end
		elif len(genes) > 0:
			outTable.write(prevChr +"\t" +prevStart +"\t" +prevEnd + "\t")
			for gsym in genes:
				outTable.write(gsym + ", " )
			outTable.write("\t" + prevStatus + "\n")
			prevChr = ''
			prevStatus = ''
			genes = []

	if len(genes) > 0:
        	outTable.write(prevChr +"\t" +prevStart +"\t" +prevEnd + "\t")
        	for gsym in genes:
                	outTable.write(gsym + ", ")
        	outTable.write("\t" + prevStatus + "\n")

	filteredTable.close()
	bedOut.close()
	outTable.close()