#!/usr/bin/python # -*- coding: utf-8 -*- ###################################################### ### -------------------- HELP -------------------- ### ''' NAME %(progname)s VERSION %(version)s CATEGORY Metabolism AUTHORS Quentin DA COSTA Jonathan VERNEAU DESCRIPTION Create a file that contains data returned by getAllReactions method: reactions and compounds list. Determines also the list of arcs. OUTPUT FORMAT The program returns a tab-delimited text file with one row per node. Columns: 1. NODES Normal/reverse reactions (RXN ID) and compounds names. 2. Object type Node type: reaction or compound. 3. Exclusion attribute Reaction or compound excluded during the reconstruction of metabolic network. 4. Label Compounds. 8. FORMULA + List of arcs: substrate - (normal or reverse) reaction (normal or reverse) reaction - product If -n argument is specified: Create a file that contains the list of nodes: reactions (RXN IDs, EC numbers), compounds (scientist names, common names, CPD IDs). 1. query Reactions (RXN IDs, EC numbers). Compounds (scientist names, common names, CPD IDs). 2. id RXN IDs, compounds names. 3. qualifier Type of node. 4. name Reactions, compounds. ''' ########################################################## ### -------------------- PACKAGES -------------------- ### import suds import time import argparse import sys import os import re ########################################################### ### -------------------- FUNCTIONS -------------------- ### def reactions(): print "Running getAllReactions on GenoScope Web service..." ## Open a connection to the GenoScope Web services url='http://www.genoscope.cns.fr/microcyc-webservice/services/fr.genoscope.agc.microcyc.business.MicrocycService.wsdl' client=suds.client.Client(url, timeout=3600) ## Running getAllReactions on GenoScope Web service reactions=client.service.getAllReactions().reactionSimpleVO return reactions def Create_file(fileName, reactions): print "Running getCompoundSimple on GWs for each compound (this may take a long time)\nand writing data in file", fileName+"..." ## Open the file "fileName" in write mode File=open(fileName, "w") File.write(';' + str.join(" ", sys.argv)+'\n') File.write(';\n') File.write(';Time: '+time.strftime('%Y-%m-%d %H:%M\n',time.localtime())) File.write(';\n') ## If -n argument is specified if args.nodes: ## Print detail of column content. Not very useful for the time being since we only have two output fields, but can be useful in general when some files wil have many columns header=""";Column content ;\t1\tquery ;\t2\tid ;\t3\tqualifier ;\t4\tname ; """ File.write(header) ## Write header line File.write(";query\tid\tqualifier\tname\n") url='http://www.genoscope.cns.fr/microcyc-webservice/services/fr.genoscope.agc.microcyc.business.MicrocycService.wsdl' client=suds.client.Client(url, timeout=3600) ## Regular expression matching html tag htmlTag = re.compile('<[^>]*>|&|;') ## Creation of an empty list compoundsList=[] ## Create a list from an integer (number of reactions): range(10)=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9] for i in range(len(reactions)): ## Retrieve frame, EC number and common name of reaction number i frame=str(reactions[i].frame) ecNumber=str(reactions[i].ecNumber) commonName=str(reactions[i].commonName) ## If commonName and ecNumber are worth "NIL", write one line for frame if commonName=="NIL" and ecNumber=="NIL": line=frame+"\t"+frame+"\treactions\tNA\n" ## If commonName is worth "NIL", write one line for frame and one for EC number elif commonName=="NIL": line=frame+"\t"+frame+"\treactions\tNA\n"+ecNumber+"\t"+frame+"\tEC\tNA\n" ## If ecNumber is worth "NIL", write one line for frame and one for common name elif ecNumber=="NIL": line=frame+"\t"+frame+"\treactions\t"+commonName+"\n"+commonName+"\t"+frame+"\treactions\t"+commonName+"\n" ## Else write one line for frame, one for common name and one for EC number else: commonName=htmlTag.sub("", commonName) line=frame+"\t"+frame+"\treactions\t"+commonName+"\n"+commonName+"\t"+frame+"\treactions\t"+commonName+"\n"+ecNumber+"\t"+frame+"\tEC\t"+commonName+"\n" File.write(line) ## If there are left compounds... if reactions[i].leftCompounds!=None: leftCompounds=reactions[i].leftCompounds.reactionParticipantSimpleVO for lC in leftCompounds: ## Retrieve compoundFrame of lC compoundFrame=str(lC.compoundFrame) ## Remove "|" character if it is in compoundFrame compoundFrame=compoundFrame.replace("|", "") ## If compoundFrame is not in compoundsList... if compoundFrame not in compoundsList: ## Add the compound to the list of compounds compoundsList.append(compoundFrame) ## Running getCompoundSimple for the lC compoundId on GenoScope Web service CompoundSimple=client.service.getCompoundSimple(lC.compoundId) ## If "commonName" attribute is part of the keys list (print dir(CompoundSimple) to see different methods of CompoundSimple) if "commonName" in CompoundSimple.__keylist__: compoundName=str(CompoundSimple.commonName) ## Replace htmlTag by nothing compoundName=htmlTag.sub("", compoundName) ## If compoundFrame is different from compoundName, write two lines, else write one (prevent the repetition of two identical rows) if compoundFrame!=compoundName: line=compoundFrame+"\t"+compoundFrame+"\tcompounds\t"+compoundName+"\n"+compoundName+"\t"+compoundFrame+"\tcompounds\t"+compoundName+"\n" else: line=compoundFrame+"\t"+compoundFrame+"\tcompounds\t"+compoundFrame+"\n" ## Else write one line without common name else: line=compoundFrame+"\t"+compoundFrame+"\tcompounds\tNA\n" File.write(line) ## If there are right compounds if reactions[i].rightCompounds!=None: rightCompounds=reactions[i].rightCompounds.reactionParticipantSimpleVO for rC in rightCompounds: compoundFrame=str(rC.compoundFrame) compoundFrame=compoundFrame.replace("|", "") if compoundFrame not in compoundsList: compoundsList.append(compoundFrame) CompoundSimple=client.service.getCompoundSimple(rC.compoundId) if "commonName" in CompoundSimple.__keylist__: compoundName=str(CompoundSimple.commonName) compoundName=htmlTag.sub("", compoundName) if compoundName!=compoundFrame: line=compoundFrame+"\t"+compoundFrame+"\tcompounds\t"+compoundName+"\n"+compoundName+"\t"+compoundFrame+"\tcompounds\t"+compoundName+"\n" else: line=compoundFrame+"\t"+compoundFrame+"\tcompounds\t"+compoundFrame+"\n" else: line=compoundFrame+"\t"+compoundFrame+"\tcompounds\tNA\n" File.write(line) ## If -n argument is not specified else: header=""";Column content ;\t1\tNODES ;\t2\tObject type ;\t3\tExclusion attribute ;\t4\tLabel ;\t5\tPubChem ;\t6\tCAS ;\t7\tKEGG_identifier ;\t8\tFORMULA ; """ File.write(header) ## Write header line File.write(";NODES\tObject type\tExclusion attribute\tLabel\tPubChem\tCAS\tKEGG_identifier\tFORMULA\n") url='http://www.genoscope.cns.fr/microcyc-webservice/services/fr.genoscope.agc.microcyc.business.MicrocycService.wsdl' client=suds.client.Client(url) htmlTag = re.compile('<[^>]*>|&|;') compoundsList=[] arcs=";ARCS\n" ## Create a list from an integer: range(10)=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9] for i in range(len(reactions)): reactionFrame=str(reactions[i].frame) ## Write two lines by reaction (normal and reverse) line=reactionFrame+">\tReaction\t"+reactionFrame+"\tNA\tNA\tNA\tNA\tNA\n"+reactionFrame+"<\tReaction\t"+reactionFrame+"\tNA\tNA\tNA\tNA\tNA\n" File.write(line) if reactions[i].leftCompounds!=None: leftCompounds=reactions[i].leftCompounds.reactionParticipantSimpleVO for lC in leftCompounds: compoundFrame=str(lC.compoundFrame) compoundFrame=compoundFrame.replace("|", "") ## Two arcs by reaction and compound (normal and reverse) arc=compoundFrame+"\t"+reactionFrame+">\n"+reactionFrame+"<\t"+compoundFrame+"\n" arcs+=arc if compoundFrame not in compoundsList: compoundsList.append(compoundFrame) CompoundSimple=client.service.getCompoundSimple(lC.compoundId) if "commonName" in CompoundSimple.__keylist__: labelCompound=str(CompoundSimple.commonName) labelCompound=htmlTag.sub("", labelCompound) else: labelCompound="NA" ## If "inchi" attribute is part of the keys list if "inchi" in CompoundSimple.__keylist__: inchi=str(CompoundSimple.inchi) if inchi=="NIL": inchi="NA" else: inchi="NA" line=compoundFrame+"\tCompound\t"+compoundFrame+"\t"+labelCompound+"\tNA\tNA\tNA\t"+inchi+"\n" File.write(line) if reactions[i].rightCompounds!=None: rightCompounds=reactions[i].rightCompounds.reactionParticipantSimpleVO for rC in rightCompounds: compoundFrame=str(rC.compoundFrame) compoundFrame=compoundFrame.replace("|", "") arc=reactionFrame+">\t"+compoundFrame+"\n"+compoundFrame+"\t"+reactionFrame+"<\n" arcs+=arc if compoundFrame not in compoundsList: compoundsList.append(compoundFrame) CompoundSimple=client.service.getCompoundSimple(rC.compoundId) if "commonName" in CompoundSimple.__keylist__: labelCompound=str(CompoundSimple.commonName) labelCompound=htmlTag.sub("", labelCompound) else: labelCompound="NA" if "inchi" in CompoundSimple.__keylist__: inchi=str(CompoundSimple.inchi) if inchi=="NIL": inchi="NA" else: inchi="NA" line=compoundFrame+"\tCompound\t"+compoundFrame+"\t"+labelCompound+"\tNA\tNA\tNA\t"+inchi+"\n" File.write(line) # print compoundsList ## Write arcs at the end of file File.write(arcs) ## Close file File.close ############################################################## ### -------------------- MAIN PROGRAM -------------------- ### if __name__=="__main__": ## Read command line arguments parser = argparse.ArgumentParser(version='12.04',add_help=0) parser.add_argument("-h", "--help", action="store_true", dest="help", help="Show this help message and exit") parser.add_argument('-o', '--outputfile', action= "store", dest="file", metavar='#', default="MICROME_v15_directed-metab-network.tab", help="Name of the output file") parser.add_argument("-n", "--nodes", action="store_true", dest="nodes", help="Create a file that contain nodes (reactions and compounds with their ID: EC number, RXN and CPD)") args = parser.parse_args() ## Function help in arguments parser if args.help: doc = globals()['__doc__'] % {'version' : parser.version, 'progname' : parser.prog} print doc parser.print_help() sys.exit(0) time1=time.time() ## Necessary functions called reactions=reactions() Create_file(args.file, reactions) ## Record end-time execution of programm time2=time.time() print 'Writing completed in',"%.2f" % (time2-time1),'seconds' print "File created in", os.getcwd().replace('\\','/')