def send_query(self, query):
if self.makeSocket():
self.soc.send(query)
else:
printf("ERROR\tCannot create or connect socket\n")
def getReactionListLines(self):
my_base_pathways = self.call_func("all-pathways :all T")
pwy_count=0
unique_rxns ={}
if self.DEBUG:
printf("Extracting the reaction list..\n")
for pathway in my_base_pathways:
if self.DEBUG:
printf(" " + pathway)
sys.stdout.flush()
pwy_count +=1
mygenes = self.genes_of_pathway(pathway,'T')
totalrxns = self.get_slot_values(pathway, "REACTION-LIST")
for rxn in totalrxns:
unique_rxns[rxn] = 1
pathway_common_name = self.get_slot_value(pathway,"common-name")
if not pathway_common_name:
pathway_common_name = "?"
num_reactions = len(totalrxns)
num_predicted_orfs = len(mygenes)
num_covered_rxns =0
num_genes =0
orf_strings = {}
for reaction in totalrxns :
rngenes = self.genes_of_reaction(reaction,"T")
rxngenes = []
for rngene in rngenes:
rxngenes.append(self.get_slot_value(rngene,"common-name"))
if rxngenes: # this reaction is covered
num_covered_rxns+= 1
rxn_name = self.get_slot_value(reaction,"common-name")
if not rxn_name:
rxn_name = '???'
if reaction in unique_rxns:
unique_rxns[reaction]= {}
unique_rxns[reaction]['name'] = rxn_name
unique_rxns[reaction]['ORFs'] = rxngenes
if rxngenes:
unique_rxns[reaction]['covered']= 1
else :
unique_rxns[reaction]['covered']= 0
unique_rxns[reaction]['num_pwys']= 1
else :
unique_rxns[reaction]['covered']= 1
unique_rxns[reaction]['num_pwys']+=1
num_genes += len(rxngenes);
for rxngene in rxngenes:
orf_strings[rxngene] =1
# done for the reactions in a pathway
outputstr = "PWY:" + "\t" + pathway + "\t" + pathway_common_name \
+ "\t" + str(num_reactions) + "\t" + str(num_covered_rxns) + "\t" + str(num_predicted_orfs)
for orf_string in orf_strings.keys():
outputstr += "\t" + orf_string
outputstr += "\n";
# printing the reactions MOST important part of the calculation
rxnOutputStrings=[]
for reaction in unique_rxns.keys():
rxnOutputStr = reaction + "\t" + unique_rxns[reaction]['name']
for orf in unique_rxns[reaction]['ORFs']:
rxnOutputStr += "\t" + orf
rxnOutputStrings.append(rxnOutputStr)
return rxnOutputStrings
def sendStartSignal(self):
if self.DEBUG:
printf("Starting up pathway tools\n")
process = Process(target=startUpPathwayTools, args=(self._ptoolsExec,))
process.start()
def send_query(self, query):
if self.makeSocket():
self.soc.send(query)
else:
printf("ERROR\tCannot create or connect socket\n")
def getReactionListLines(self):
my_base_pathways = self.call_func("all-pathways :all T")
pwy_count = 0
unique_rxns = {}
if self.DEBUG:
printf("INFO\tExtracting the reaction list\n")
for pathway in my_base_pathways:
if self.DEBUG:
printf(" " + pathway)
sys.stdout.flush()
pwy_count += 1
mygenes = self.genes_of_pathway(pathway, 'T')
totalrxns = self.get_slot_values(pathway, "REACTION-LIST")
for rxn in totalrxns:
unique_rxns[rxn] = 1
pathway_common_name = self.get_slot_value(pathway, "common-name")
if not pathway_common_name:
pathway_common_name = "?"
num_reactions = len(totalrxns)
num_predicted_orfs = len(mygenes)
num_covered_rxns = 0
num_genes = 0
orf_strings = {}
for reaction in totalrxns:
rngenes = self.genes_of_reaction(reaction, "T")
rxngenes = []
for rngene in rngenes:
rxngenes.append(self.get_slot_value(rngene, "common-name"))
if rxngenes: # this reaction is covered
num_covered_rxns += 1
rxn_name = self.get_slot_value(reaction, "common-name")
if not rxn_name:
rxn_name = '???'
if reaction in unique_rxns:
unique_rxns[reaction] = {}
unique_rxns[reaction]['name'] = rxn_name
unique_rxns[reaction]['ORFs'] = rxngenes
if rxngenes:
unique_rxns[reaction]['covered'] = 1
else:
unique_rxns[reaction]['covered'] = 0
unique_rxns[reaction]['num_pwys'] = 1
else:
unique_rxns[reaction]['covered'] = 1
unique_rxns[reaction]['num_pwys'] += 1
num_genes += len(rxngenes)
for rxngene in rxngenes:
orf_strings[rxngene] = 1
# done for the reactions in a pathway
outputstr = "PWY:" + "\t" + pathway + "\t" + pathway_common_name \
+ "\t" + str(num_reactions) + "\t" + str(num_covered_rxns) + "\t" + str(num_predicted_orfs)
for orf_string in orf_strings.keys():
outputstr += "\t" + orf_string
outputstr += "\n"
# printing the reactions MOST important part of the calculation
rxnOutputStrings = []
for reaction in unique_rxns.keys():
rxnOutputStr = reaction + "\t" + unique_rxns[reaction]['name']
for orf in unique_rxns[reaction]['ORFs']:
rxnOutputStr += "\t" + orf
rxnOutputStrings.append(rxnOutputStr)
return rxnOutputStrings
def sendStartSignal(self):
if self.DEBUG:
printf("INFO\tStarting up pathway tools\n")
process = Process(target=startUpPathwayTools,
args=(self._ptoolsExec, ))
process.start()
