comparison rank_pathways_pct.py @ 27:8997f2ca8c7a

Update to Miller Lab devshed revision bae0d3306d3b

26:91e835060ad2

#!/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

#       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()

27:8997f2ca8c7a

#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
#       KEGGFisher.py
#       
#       Copyright 2013 Oscar Reina <[e-mail]>
#       
#       This program is free software; you can redistribute it and/or modify
#       it under the pathways 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

#       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 as fisher
from decimal import Decimal,getcontext
from math import lgamma,exp,factorial

def binProb(SAPs_KEGG,NoSAPs_KEGG,SAPs_all,NoSAPs_all,CntKEGG_All,totalSAPs,pKEGG):
	"""
	Returns binomial probability.
	"""
	def comb(CntKEGG_All,k):
		return factorial(CntKEGG_All) / Decimal(str(factorial(k)*factorial(CntKEGG_All-k)))
	probLow = 0
	for k in range(0, SAPs_KEGG+1):
		cp=Decimal(str(comb(CntKEGG_All,k)))
		bp=Decimal(str(pKEGG**k))
		dp=Decimal(str(1.0-pKEGG))**Decimal(str(CntKEGG_All-k))
		probLow+=cp*bp*dp
	#~ 
	probHigh = 0
	for k in range(int(SAPs_KEGG),CntKEGG_All+1):
		cp=Decimal(str(comb(CntKEGG_All,k)))
		bp=Decimal(str(pKEGG**k))
		dp=Decimal(str(1.0-pKEGG))**Decimal(str(CntKEGG_All-k))
		probHigh+=cp*bp*dp
	return probLow,probHigh

def gauss_hypergeom(X, CntKEGG_All, SAPs_all, totalSAPs):
	CntKEGG_All,SAPs_all,totalSAPs
	"""
	Returns the probability of drawing X successes of SAPs_all marked items
	in CntKEGG_All draws from a bin of totalSAPs total items
	"""
	def logchoose(ni, ki):
		try:
			lgn1 = lgamma(ni+1)
			lgk1 = lgamma(ki+1)
			lgnk1 = lgamma(ni-ki+1)
		except ValueError:
			raise ValueError
		return lgn1 - (lgnk1 + lgk1)
	#~ 
	r1 = logchoose(SAPs_all, X)
	try:
		r2 = logchoose(totalSAPs-SAPs_all, CntKEGG_All-X)
	except ValueError:
		return 0
	r3 = logchoose(totalSAPs,CntKEGG_All)
	return exp(r1 + r2 - r3)
    
def hypergeo_sf(SAPs_KEGG,NoSAPs_KEGG,SAPs_all,NoSAPs_all,CntKEGG_All,totalSAPs,pKEGG):
	"""
	Runs Hypergeometric probability test
	"""
	s = 0
	t=0
	for i in range(SAPs_KEGG,min(SAPs_all,CntKEGG_All)+1):
		s += max(gauss_hypergeom(i,CntKEGG_All,SAPs_all,totalSAPs), 0.0)
	for i in range(0, SAPs_KEGG+1):
		t += max(gauss_hypergeom(i,CntKEGG_All,SAPs_all,totalSAPs), 0.0)
	return min(max(t,0.0), 1),min(max(s,0.0), 1)

def fisherexct(SAPs_KEGG,NoSAPs_KEGG,SAPs_all,NoSAPs_all,CntKEGG_All,totalSAPs,pKEGG):
	"""
	Runs Fisher's exact test
	"""
	ftest=fisher(SAPs_KEGG,NoSAPs_KEGG,SAPs_all,NoSAPs_all)
	probLow,probHigh=ftest.left_tail,ftest.right_tail
	return probLow,probHigh

def rtrnKEGGcENSEMBLc(inBckgrndfile,columnENSEMBLTBckgrnd,columnKEGGBckgrnd):
	"""
	"""
	dKEGGTENSEMBLT={}
	for eachl in open(inBckgrndfile,'r'):
		if eachl.strip():
			ENSEMBLT=eachl.splitlines()[0].split('\t')[columnENSEMBLTBckgrnd]
			KEGGTs=set(eachl.splitlines()[0].split('\t')[columnKEGGBckgrnd].split('.'))
			KEGGTs=KEGGTs.difference(set(['','U','N']))
			for KEGGT in KEGGTs:
				try:
					dKEGGTENSEMBLT[KEGGT].add(ENSEMBLT)
				except:
					dKEGGTENSEMBLT[KEGGT]=set([ENSEMBLT])
	ENSEMBLTGinKEGG=set.union(*dKEGGTENSEMBLT.values())
	return dKEGGTENSEMBLT,ENSEMBLTGinKEGG

def rtrnENSEMBLcSAPs(inSAPsfile,columnENSEMBLT,ENSEMBLTGinKEGG):
	"""
	returns a set of the ENSEMBLT codes present in the input list and
	in the KEGG file
	"""
	sENSEMBLTSAPsinKEGG=set()
	for eachl in open(inSAPsfile,'r'):
		ENSEMBLT=eachl.splitlines()[0].split('\t')[columnENSEMBLT]
		if ENSEMBLT in ENSEMBLTGinKEGG:
			sENSEMBLTSAPsinKEGG.add(ENSEMBLT)
	return sENSEMBLTSAPsinKEGG

def rtrnCounts(dKEGGTENSEMBLT,ENSEMBLTGinKEGG,sENSEMBLTSAPsinKEGG,statsTest):
	"""
	returns a list of the ENSEMBLT codes present in the input list and
	in the KEGG file. The pathways in this list are: 'Go Term','# Genes in
	the KEGG Term','# Genes in the list and in the KEGG Term','Enrichement
	of the KEGG Term for genes in the input list','Genes in the input list
	present in the KEGG term'
	"""
	totalSAPs=len(ENSEMBLTGinKEGG)
	SAPs_all=len(sENSEMBLTSAPsinKEGG)
	NoSAPs_all=totalSAPs-SAPs_all
	pKEGG=SAPs_all/float(totalSAPs)
	#~ 
	lp=len(dKEGGTENSEMBLT)
	cnt=0
	#~ 
	if statsTest=='fisher':
		ptest=fisherexct
	elif statsTest=='hypergeometric':
		ptest=hypergeo_sf
	elif statsTest=='binomial':
		ptest=binProb
	#~ 
	ltfreqs=[]
	for echKEGGT in dKEGGTENSEMBLT:
		cnt+=1
		CntKEGG_All=len(dKEGGTENSEMBLT[echKEGGT])
		SAPs_KEGG=len(dKEGGTENSEMBLT[echKEGGT].intersection(sENSEMBLTSAPsinKEGG))
		NoSAPs_KEGG=CntKEGG_All-SAPs_KEGG
		probLow,probHigh=ptest(SAPs_KEGG,NoSAPs_KEGG,SAPs_all,NoSAPs_all,CntKEGG_All,totalSAPs,pKEGG)
		ltfreqs.append([(SAPs_KEGG/Decimal(CntKEGG_All)),SAPs_KEGG,probLow,probHigh,echKEGGT])
	#~ 
	ltfreqs.sort()
	ltfreqs.reverse()
	outl=[]
	cper,crank=Decimal('2'),0
	#~ 
	getcontext().prec=2#set 2 decimal places
	for perc,cnt_go,pvalLow,pvalHigh,goTerm in ltfreqs:
		if perc<cper:
			crank+=1
			cper=perc
		outl.append('\t'.join([str(cnt_go),str(Decimal(perc)*Decimal('1.0')),str(crank),str(Decimal(pvalLow)*Decimal('1.0')),str(Decimal(pvalHigh)*Decimal('1.0')),goTerm]))
	#~ 
	return outl
	

def main():
	#~ 
	parser = argparse.ArgumentParser(description='Returns the count of genes in KEGG categories and their statistical overrrepresentation, from a list of genes and an background file (i.e. plane text with ENSEMBLT and KEGG pathways).')
	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('--inBckgrndfile',metavar='input TXT file',type=str,help='the input file with the background 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('--columnENSEMBLTBckgrnd',metavar='column number',type=int,help='column with the ENSEMBL transcript code in the background file.',required=True)
	parser.add_argument('--columnKEGGBckgrnd',metavar='column number',type=int,help='column with the KEGG pathways in the background file.',required=True)
	parser.add_argument('--statsTest',metavar='input TXT file',type=str,help='statistical test to compare KEGG pathways (i.e. fisher, hypergeometric, binomial).',required=True)

	args = parser.parse_args()

	inSAPsfile = args.input
	inBckgrndfile = args.inBckgrndfile
	saleKEGGPCount = args.output
	columnENSEMBLT = args.columnENSEMBLT
	columnENSEMBLTBckgrnd = args.columnENSEMBLTBckgrnd
	columnKEGGBckgrnd = args.columnKEGGBckgrnd
	statsTest = args.statsTest
	columnENSEMBLT-=1
	columnENSEMBLTBckgrnd-=1
	columnKEGGBckgrnd=-1
	#~ 
	dKEGGTENSEMBLT,ENSEMBLTGinKEGG=rtrnKEGGcENSEMBLc(inBckgrndfile,columnENSEMBLTBckgrnd,columnKEGGBckgrnd)
	sENSEMBLTSAPsinKEGG=rtrnENSEMBLcSAPs(inSAPsfile,columnENSEMBLT,ENSEMBLTGinKEGG)
	outl=rtrnCounts(dKEGGTENSEMBLT,ENSEMBLTGinKEGG,sENSEMBLTSAPsinKEGG,statsTest)
	#~ 
	saleKEGGPCount=open(saleKEGGPCount,'w')
	saleKEGGPCount.write('\n'.join(outl))
	saleKEGGPCount.close()
	#~ 
	return 0

if __name__ == '__main__':
	main()