diff rank_pathways_pct.py @ 22:95a05c1ef5d5

update to devshed revision aaece207bd01

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rank_pathways_pct.py	Mon Mar 11 11:28:06 2013 -0400
@@ -0,0 +1,138 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+#       calcfreq.py
+#       
+#       Copyright 2011 Oscar Bedoya-Reina <[e-mail]>
+#       
+#       This program 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 2 of the License, or
+#       (at your option) any later version.
+#       
+#       This program 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 this program; if not, write to the Free Software
+#       Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+#       MA 02110-1301, USA.
+
+import argparse,os,sys
+from decimal import Decimal,getcontext
+from LocationFile import LocationFile
+from fisher import pvalue
+
+#method to rank the the pthways by mut. freq.
+def rankd(ltfreqs):
+	ordvals=sorted(ltfreqs)#sort and reverse freqs.
+	#~ 
+	outrnk=[]
+	tmpFreq0,tmpCount,pval,tmpPthw=ordvals.pop()#the highest possible value
+	crank=1
+	outrnk.append('\t'.join([str(tmpCount),str(tmpFreq0),str(crank),str(pval),tmpPthw]))
+	totalnvals=len(ordvals)
+	cnt=0
+	while totalnvals>cnt:
+		cnt+=1
+		tmpFreq,tmpCount,pval,tmpPthw=ordvals.pop()
+		if tmpFreq!=tmpFreq0:
+			crank=len(outrnk)+1
+			tmpFreq0=tmpFreq
+		outrnk.append('\t'.join([str(tmpCount),str(tmpFreq),str(crank),str(pval),tmpPthw]))
+	return outrnk
+		
+
+def main():
+	parser = argparse.ArgumentParser(description='Obtain KEGG images from a list of genes.')
+	parser.add_argument('--input',metavar='input TXT file',type=str,help='the input file with the table in txt format')
+	parser.add_argument('--output',metavar='output TXT file',type=str,help='the output file with the table in txt format. Column 1 is the count of genes in the list, Column 2 is the percentage of the pathway genes present on the list. Column 3 is the rank based on column 2')
+	parser.add_argument('--posKEGGclmn',metavar='column number',type=int,help='the column with the KEGG pathway code/name')
+	parser.add_argument('--KEGGgeneposcolmn',metavar='column number',type=int,help='column with the KEGG gene code')
+	parser.add_argument('--loc_file',metavar='location file',type=str,help='location file')
+	parser.add_argument('--species',metavar='species',type=str,help='species')
+	#~Open arguments 
+	class C(object):
+		pass
+	fulargs=C()
+	parser.parse_args(sys.argv[1:],namespace=fulargs)
+	#test input vars
+	inputf,outputf,posKEGGclmn,Kgeneposcolmn=fulargs.input,fulargs.output,fulargs.posKEGGclmn,fulargs.KEGGgeneposcolmn
+	locf,species=fulargs.loc_file,fulargs.species
+	#make a dictionary of valid genes
+	posKEGGclmn-=1
+	Kgeneposcolmn-=1
+	dKEGGcPthws=dict([(x.split('\t')[Kgeneposcolmn],set(x.split('\t')[posKEGGclmn].split('.'))) for x in open(inputf).read().splitlines()[1:] if x.split('\t')[posKEGGclmn] not in set(['U','N'])])
+	for u in ['U','N']:
+		try:
+			a=dKEGGcPthws.pop(u)
+		except:
+			pass
+	getcontext().prec=2#set 2 decimal places
+	sdGenes=set([x for x in dKEGGcPthws.keys() if x.find('.')>-1])
+	while True:#to correct names with more than one gene
+		try:
+			mgenes=sdGenes.pop()
+			pthwsAssotd=dKEGGcPthws.pop(mgenes)
+			mgenes=mgenes.split('.')
+			for eachg in mgenes:
+				dKEGGcPthws[eachg]=pthwsAssotd
+		except:
+			break
+	#~ Count genes
+
+	location_file = LocationFile(locf)
+	prefix, kxml_dir_path, dict_file = location_file.get_values(species)
+	dPthContsTotls = {}
+	try:
+	    with open(dict_file) as fh:
+	        for line in fh:
+	            line = line.rstrip('\r\n')
+	            value, key = line.split('\t')
+	            dPthContsTotls[key] = int(value)
+	except IOError, err:
+	    print >> sys.stderr, 'Error opening dict file {0}: {1}'.format(dict_file, err.strerror)
+	    sys.exit(1)
+	
+	dPthContsTmp=dict([(x,0) for x in dPthContsTotls.keys()])#create a list of genes
+	sdGenes=set(dKEGGcPthws.keys())#list of all genes
+	cntGens=0
+	ltGens=len(sdGenes)
+	while cntGens<ltGens:
+		cGen=sdGenes.pop()
+		sKEGGcPthws=dKEGGcPthws.pop(cGen)
+		for eachP in sKEGGcPthws:
+			if eachP!='N':
+				if eachP in dPthContsTmp:
+					dPthContsTmp[eachP]+=1
+				else:
+					print >> sys.stderr, "Error: pathway not found in database: '{0}'".format(eachP)
+					sys.exit(1)
+		cntGens+=1
+	#~ Calculate Freqs.
+	ltfreqs=[]
+	cntAllKEGGinGnm=sum(dPthContsTotls.values())
+	cntListKEGGinGnm=sum(dPthContsTmp.values())
+	cntAllKEGGNOTinGnm=cntAllKEGGinGnm-cntListKEGGinGnm
+	for pthw in dPthContsTotls:
+		cntAllKEGGinpthw=Decimal(dPthContsTotls[pthw])
+		try:
+			cntListKEGGinpthw=Decimal(dPthContsTmp[pthw])
+		except:
+			cntListKEGGinpthw=Decimal('0')
+		cntAllKEGGNOTinpthw=cntAllKEGGinpthw-cntListKEGGinpthw
+		pval=pvalue(cntListKEGGinpthw,cntAllKEGGNOTinpthw,cntListKEGGinGnm,cntAllKEGGNOTinGnm)
+
+		ltfreqs.append([(cntListKEGGinpthw/cntAllKEGGinpthw),cntListKEGGinpthw,Decimal(str(pval.two_tail))*1,pthw])
+	#~ ltfreqs=[((Decimal(dPthContsTmp[x])/Decimal(dPthContsTotls[x])),Decimal(dPthContsTmp[x]),x) for x in dPthContsTotls]
+	tabllfreqs='\n'.join(rankd(ltfreqs))
+	salef=open(outputf,'w')
+	salef.write(tabllfreqs)
+	salef.close()
+	return 0
+	
+
+if __name__ == '__main__':
+	main()