annotate calclenchange.py @ 33:5064f618ec1c

remove munkres dependency

#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
#       calclenchange.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,mechanize,os,sys
from decimal import Decimal,getcontext
from xml.etree.ElementTree import ElementTree,tostring
import networkx as nx
from copy import copy

#method to rank the the pthways by mut. freq.
def rankdN(ltfreqs):
	ordvals=sorted(ltfreqs)#sort and reverse freqs.
	#~ 
	outrnk=[]
	tmpChng0,tmpOri,tmpMut,tmpPthw=ordvals.pop()#the highest possible value
	if tmpOri=='C':
		if tmpMut!='C':
			tmpChng0='C-%s'%tmpMut
		else:
			tmpChng0=Decimal('0')
	crank=1
	outrnk.append([str(tmpChng0),str(tmpOri),str(tmpMut),str(crank),tmpPthw])
	totalnvals=len(ordvals)
	cnt=0
	while totalnvals>cnt:
		cnt+=1
		tmpChng,tmpOri,tmpMut,tmpPthw=ordvals.pop()
		if tmpOri=='C':
			if tmpMut!='C':
				tmpChng='C-%s'%tmpMut
			else:
				tmpChng=Decimal('0')
		if tmpChng!=tmpChng0:
			crank=len(outrnk)+1
			tmpChng0=tmpChng
		outrnk.append([str(tmpChng),str(tmpOri),str(tmpMut),str(crank),tmpPthw])
	return outrnk

#method to rank the the pthways by mut. freq.
def rankdAvr(ltfreqs):
	ordvals=sorted(ltfreqs)#sort and reverse freqs.
	#~ 
	outrnk={}
	tmpChng0,tmpOri,tmpMut,tmpPthw=ordvals.pop()#the highest possible value
	if tmpOri=='I':
		if tmpMut!='I':
			tmpChng0='I-%s'%tmpMut
		else:
			tmpChng0=Decimal('0')
	crank=1
	outrnk[tmpPthw]='\t'.join([str(tmpChng0),str(tmpOri),str(tmpMut),str(crank)])
	totalnvals=len(ordvals)
	cnt=0
	while totalnvals>cnt:
		cnt+=1
		tmpChng,tmpOri,tmpMut,tmpPthw=ordvals.pop()
		if tmpOri=='I':
			if tmpMut!='I':
				tmpChng='I-%s'%tmpMut
			else:
				tmpChng=Decimal('0')
		if tmpChng!=tmpChng0:
			crank=len(outrnk)+1
			tmpChng0=tmpChng
		outrnk[tmpPthw]='\t'.join([str(tmpChng),str(tmpOri),str(tmpMut),str(crank)])
	return outrnk

#this method takes as input a list of pairs of edges(beginNod,endNod) and returns a list of nodes with indegree 0 and outdegree 0
def returnstartanendnodes(edges):
	listID0st=set()#starts
	listOD0en=set()#end
	for beginNod,endNod in edges:# O(n)
		listID0st.add(beginNod)
		listOD0en.add(endNod)
	startNdsID0=listID0st.difference(listOD0en)
	endNdsOD0=listOD0en.difference(listID0st)
	return startNdsID0,endNdsOD0

#~ Method to return nodes and edges
def returnNodesNEdgesfKXML(fpthwKGXML):
	#~ 
	tree = ElementTree()
	ptree=tree.parse(fpthwKGXML)
	#~ 
	title=ptree.get('title')
	prots=ptree.findall('entry')
	reactns=ptree.findall('reaction')
	#~ 
	edges,ndstmp=set(),set()
	nreactns=len(reactns)
	cr=0#count reacts
	while nreactns>cr:
		cr+=1
		reactn=reactns.pop()
		mainid=reactn.get('id')
		ndstmp.add(mainid)#add node
		reacttyp=reactn.get('type')
		sbstrts=reactn.findall('substrate')
		while len(sbstrts)>0:
			csbstrt=sbstrts.pop()
			csbtsid=csbstrt.get('id')
			ndstmp.add(csbtsid)#add node
			if reacttyp=='irreversible':
				edges.add((csbtsid,mainid))#add edges
			elif reacttyp=='reversible':
				edges.add((mainid,csbtsid))#add edges
				edges.add((csbtsid,mainid))#add edges
		#~ 
		prdcts=reactn.findall('product')
		while len(prdcts)>0:
			prdct=prdcts.pop()
			prodctid=prdct.get('id')
			ndstmp.add(prodctid)#add node
			if reacttyp=='irreversible':
				edges.add((mainid,prodctid))#add edges
			elif reacttyp=='reversible':
				edges.add((mainid,prodctid))#add edges
				edges.add((prodctid,mainid))#add edges
	#~ Nodes
	nprots=len(prots)
	cp=0#count prots
	dnodes={}
	while nprots>cp:
		cp+=1
		prot=prots.pop()
		tmpProtnm=prot.get('id')
		if tmpProtnm in ndstmp:
			dnodes[prot.get('id')]=set(prot.get('name').split())#each genename for each Id
	return dnodes,edges,title

#~ make calculation on pathways
def rtrnAvrgLen(edges,strNds,endNds):
	wG=nx.DiGraph()#reference graph
	wG.add_edges_from(edges)
	dPairsSrcSnks=nx.all_pairs_shortest_path_length(wG)#dictionary between sources and sink and length
	nstartNdsID0=len(strNds)
	cstrtNds=0
	nPaths=0
	lPathLen=[]
	while nstartNdsID0>cstrtNds:
		cStartNd=strNds.pop()#current start node
		dEndNdsLen=dPairsSrcSnks.pop(cStartNd)
		for cendNd in dEndNdsLen:
			if cendNd in endNds:
				lPathLen.append(dEndNdsLen[cendNd])
				nPaths+=1
		cstrtNds+=1
	AvrgPthLen=0
	if nPaths!=0:
		AvrgPthLen=Decimal(sum(lPathLen))/Decimal(str(nPaths))
	return nPaths,AvrgPthLen

def main():
	parser = argparse.ArgumentParser(description='Rank pathways based on the change in length and number of paths connecting sources and sinks.')
	parser.add_argument('--loc_file',metavar='correlational database',type=str,help='correlational database')
	parser.add_argument('--species',metavar='species name',type=str,help='the species of interest in loc_file')
	parser.add_argument('--output',metavar='output TXT file',type=str,help='the output file with the table in txt format. Column 1 is the diference between column 2 and column 3, Column 2 is the pathway average length (between sources and sinks) including the genes in the input list, Column 3 is the pathway average length EXCLUDING the genes in the input list, Column 4 is the rank based on column 1. Column 5 is the diference between column 6 and column 7, Column 6 is the number of paths between sources and sinks, including the genes in the input list, Column 7 is the number of paths between sources and sinks EXCLUDING the genes in the input list, Column 8 is the rank based on column 5. Column 9 I the pathway name' )
	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('--input',metavar='input TXT file',type=str,help='the input file with the table in txt format')
	#~ 
	#~Open arguments 
	class C(object):
		pass
	fulargs=C()
	parser.parse_args(sys.argv[1:],namespace=fulargs)
	#test input vars
	inputf,loc_file,species,output,posKEGGclmn,Kgeneposcolmn=fulargs.input,fulargs.loc_file,fulargs.species,fulargs.output,fulargs.posKEGGclmn,fulargs.KEGGgeneposcolmn
	posKEGGclmn-=1#correct pos
	Kgeneposcolmn-=1
	#~ Get the extra variables
	crDB=[x.split() for x in open(loc_file).read().splitlines() if x.split()[0]==species][0]
	sppPrefx,dinput=crDB[1],crDB[2]
	#~ set decimal positions
	getcontext().prec = 3
	#make a dictionary of valid genes
	dKEGGcPthws=dict([(x.split('\t')[Kgeneposcolmn],set([y.split('=')[0] for y in x.split('\t')[posKEGGclmn].split('.')])) for x in open(inputf).read().splitlines()[1:] if x.strip()])
	sdGenes=set([x for x in dKEGGcPthws.keys() if x.find('.')>-1])
	while True:#to crrect 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
	#~ 
	lPthwsF=[x for x in os.listdir(dinput) if x.find('.xml')>-1 if x not in ['cfa04070.xml']]
	nPthws=len(lPthwsF)
	cPthw=0
	lPthwPthN=[]#the output list for number of paths
	lPthwPthAvr=[]#the output list for the length of paths
	#~ 
	while cPthw<nPthws:
		cPthw+=1
		KEGGpathw=lPthwsF.pop()
		comdKEGGpathw=KEGGpathw.split('.')[0]
		tmpddGenrcgenPresent=set()
		sKEGGc=dKEGGcPthws.keys()
		lsKEGGc=len(sKEGGc)
		ctPthw=0
		while ctPthw < lsKEGGc:#to save memory
			eachK=sKEGGc.pop()
			alPthws=dKEGGcPthws[eachK]
			if comdKEGGpathw in alPthws:
				tmpddGenrcgenPresent.add(':'.join([sppPrefx,eachK]))
			ctPthw+=1
		#~ Make graph calculations	
		dnodes,edges,title=returnNodesNEdgesfKXML(open(os.path.join(dinput,KEGGpathw)))
		startNdsID0,endNdsOD0=returnstartanendnodes(edges)
		startNdsOri=copy(startNdsID0)
		#~ 
		nPaths='C'#stands for circuit
		AvrgPthLen='I'#stand for infinite
		if len(startNdsID0)>0 and len(endNdsOD0)>0:
			nPaths,AvrgPthLen=rtrnAvrgLen(edges,startNdsID0,endNdsOD0)
		#~ work with the genes in the list
		genestodel=set()
		lnodes=len(dnodes)
		sNds=set(dnodes)
		ctPthw=0
		while ctPthw<lnodes:
			ctPthw+=1
			cNod=sNds.pop()
			sgenes=dnodes.pop(cNod)
			if len(sgenes.intersection(tmpddGenrcgenPresent))==len(sgenes):
				genestodel.add(cNod)
		#~ del nodes from graph edges
		wnPaths,wAvrgPthLen=copy(nPaths),copy(AvrgPthLen)
		if len(genestodel)>0:
			wedges=set([x for x in edges if len(set(x).intersection(genestodel))==0])
			wstartNds,wendNds=returnstartanendnodes(wedges)
			if nPaths!='C':
				wstartNds=[x for x in wstartNds if x in startNdsOri]
				wendNds=[x for x in wendNds if x in endNdsOD0]
			if len(wstartNds)>0 and len(wendNds)>0:
				wnPaths,wAvrgPthLen=rtrnAvrgLen(wedges,wstartNds,wendNds)
		#~ Calculate the differences
		orNP,mutNP,oriLen,mutLen=nPaths,wnPaths,AvrgPthLen,wAvrgPthLen
		if nPaths=='C':
			orNP=Decimal('1000')
			oriLen=Decimal('1000')
		if wnPaths=='C':
			mutNP=Decimal('1000')
			mutLen=Decimal('1000')
		lPthwPthN.append([orNP-mutNP,nPaths,wnPaths,'='.join([comdKEGGpathw,title])])#print nPaths,AvrgPthLen
		lPthwPthAvr.append([oriLen-mutLen,AvrgPthLen,wAvrgPthLen,'='.join([comdKEGGpathw,title])])#print nPaths,AvrgPthLen
	doutrnkPthN=rankdN(lPthwPthN)
	doutrnkPthAvr=rankdAvr(lPthwPthAvr)
	#~ 
	sall=['\t'.join([doutrnkPthAvr[x[4]],'\t'.join(x)]) for x in doutrnkPthN]
	salef=open(output,'w')
	salef.write('\n'.join(sall))
	salef.close()
	return 0
	

if __name__ == '__main__':
	main()