--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rank_terms.py	Mon Mar 11 11:28:06 2013 -0400
@@ -0,0 +1,132 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+#       GOFisher.py
+#       
+#       Copyright 2013 Oscar Reina <oscar@niska.bx.psu.edu>
+#       
+#       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
+import os
+import sys
+from fisher import pvalue
+from decimal import Decimal,getcontext
+
+def rtrnGOcENSEMBLc(inExtnddfile,columnENSEMBLTExtndd,columnGOExtndd):
+	"""
+	"""
+	dGOTENSEMBLT={}
+	for eachl in open(inExtnddfile,'r'):
+		if eachl.strip():
+			ENSEMBLT=eachl.splitlines()[0].split('\t')[columnENSEMBLTExtndd]
+			GOTs=set(eachl.splitlines()[0].split('\t')[columnGOExtndd].split('.'))
+			GOTs=GOTs.difference(set(['','U','N']))
+			for GOT in GOTs:
+				try:
+					dGOTENSEMBLT[GOT].add(ENSEMBLT)
+				except:
+					dGOTENSEMBLT[GOT]=set([ENSEMBLT])
+	#~ 
+	##dGOTENSEMBLT.pop('')
+	ENSEMBLTGinGO=set.union(*dGOTENSEMBLT.values())
+	return dGOTENSEMBLT,ENSEMBLTGinGO
+
+def rtrnENSEMBLcSAPs(inSAPsfile,columnENSEMBLT,ENSEMBLTGinGO):
+	"""
+	returns a set of the ENSEMBLT codes present in the input list and
+	in the GO file
+	"""
+	sENSEMBLTSAPsinGO=set()
+	for eachl in open(inSAPsfile,'r'):
+		ENSEMBLT=eachl.splitlines()[0].split('\t')[columnENSEMBLT]
+		if ENSEMBLT in ENSEMBLTGinGO:
+			sENSEMBLTSAPsinGO.add(ENSEMBLT)
+	return sENSEMBLTSAPsinGO
+
+def rtrnCounts(dGOTENSEMBLT,ENSEMBLTGinGO,sENSEMBLTSAPsinGO):
+	"""
+	returns a list of the ENSEMBLT codes present in the input list and
+	in the GO file. The terms in this list are: 'Go Term','# Genes in
+	the GO Term','# Genes in the list and in the GO Term','Enrichement
+	of the GO Term for genes in the input list','Genes in the input list
+	present in the GO term'
+	"""
+	getcontext().prec=2#set 2 decimal places
+	SAPs_all=len(sENSEMBLTSAPsinGO)
+	NoSAPs_all=len(ENSEMBLTGinGO)-SAPs_all
+	#~ 
+	lp=len(dGOTENSEMBLT)
+	cnt=0
+	#~ 
+	ltfreqs=[]
+	for echGOT in dGOTENSEMBLT:
+		cnt+=1
+		##print 'Running "%s", %s out of %s'%(echGOT,cnt,lp)
+		CntGO_All=len(dGOTENSEMBLT[echGOT])
+		SAPs_GO=len(dGOTENSEMBLT[echGOT].intersection(sENSEMBLTSAPsinGO))
+		NoSAPs_GO=CntGO_All-SAPs_GO
+		pval=pvalue(SAPs_GO,NoSAPs_GO,SAPs_all,NoSAPs_all)
+		#~ outl.append('\t'.join([str(x) for x in(str(pval.two_tail),CntGO_All,SAPs_GO,'.'.join(sorted(dGOTENSEMBLT[echGOT].intersection(sENSEMBLTSAPsinGO))),echGOT)]))
+		ltfreqs.append([(SAPs_GO/Decimal(CntGO_All)),SAPs_GO,Decimal(str(pval.two_tail))*1,echGOT])
+	#~ 
+	ltfreqs.sort()
+	ltfreqs.reverse()
+	outl=[]
+	cper,crank=Decimal('2'),0
+	#~ 
+	for perc,cnt_go,pval,goTerm in ltfreqs:
+		if perc<cper:
+			crank+=1
+			cper=perc
+		outl.append('\t'.join([str(cnt_go),str(perc),str(crank),str(pval),goTerm]))
+	#~ 
+	return outl
+	
+
+def main():
+	#~ 
+	parser = argparse.ArgumentParser(description='Returns the count of genes in GO categories and their statistical overrrepresentation, from a list of genes and an extended file (i.e. plane text with ENSEMBLT and GO terms).')
+	parser.add_argument('--input',metavar='input TXT file',type=str,help='the input file with the table in txt format.',required=True)
+	parser.add_argument('--inExtnddfile',metavar='input TXT file',type=str,help='the input file with the extended table in txt format.',required=True)
+	parser.add_argument('--output',metavar='output TXT file',type=str,help='the output file with the table in txt format.',required=True)
+	parser.add_argument('--columnENSEMBLT',metavar='column number',type=int,help='column with the ENSEMBL transcript code in the input file.',required=True)
+	parser.add_argument('--columnENSEMBLTExtndd',metavar='column number',type=int,help='column with the ENSEMBL transcript code in the extended file.',required=True)
+	parser.add_argument('--columnGOExtndd',metavar='column number',type=int,help='column with the GO terms in the extended file.',required=True)
+
+	args = parser.parse_args()
+
+	inSAPsfile = args.input
+	inExtnddfile = args.inExtnddfile
+	saleGOPCount = args.output
+	columnENSEMBLT = args.columnENSEMBLT
+	columnENSEMBLTExtndd = args.columnENSEMBLTExtndd
+	columnGOExtndd = args.columnGOExtndd
+
+	#~ 
+	dGOTENSEMBLT,ENSEMBLTGinGO=rtrnGOcENSEMBLc(inExtnddfile,columnENSEMBLTExtndd,columnGOExtndd)
+	sENSEMBLTSAPsinGO=rtrnENSEMBLcSAPs(inSAPsfile,columnENSEMBLT,ENSEMBLTGinGO)
+	outl=rtrnCounts(dGOTENSEMBLT,ENSEMBLTGinGO,sENSEMBLTSAPsinGO)
+	#~ 
+	saleGOPCount=open(saleGOPCount,'w')
+	saleGOPCount.write('\n'.join(outl))
+	saleGOPCount.close()
+	#~ 
+	return 0
+
+if __name__ == '__main__':
+	main()
+