def GetWikiPaths4IDs(idList,SC):
# Function that uses a list of IDs and a systm code as input and
# returns a string with all the WikiPathways where th IDs exist (including the new lines) as tab separated fields:
# No, ID, Species, Pathway ID, Pathway Name
# Load SOAPpy and dependent modules (fpconst) and access the remote
# SOAP server through a proxy class, SOAPProxy - see:
# (http://diveintopython.org/soap_web_services/first_steps.html)
from SOAPpy import SOAPProxy
url = 'http://www.wikipathways.org/wpi/webservice/webservice.php'
namespace = 'http://www.wikipathways.org/webservice'
server = SOAPProxy(url, namespace)
# Define the order of args: needed for this service
server.config.argsOrdering = {'findPathwaysByXref': ('ids', 'codes') }
index=1 # index of the result lines
print_output = '' # output of the function
# For each ID findPathwaysByXref (multiple args; returns list of dictionary references)
for gi in idList:
# checking any erors
try:
probeset_containing = server.findPathwaysByXref(codes=SC, ids=gi)
NoPaths = len(probeset_containing)
#Loops through a list of dictionary items if results
if NoPaths > 0 :
for object in probeset_containing:
#calls select dictionary keys to print out values
print_output += str(int(index))+'\t'+str(gi)+'\t'+str(object['species'])+'\t'+str(object['id'])+'\t'+str(object['name'])+'\n'
index+=1
else:
print gi, "can't be found in WikiPathways!"
except:
#pass # if error do nothing
print gi, 'has', NoPaths, 'pathways but it can be processed!'
return print_output
# Print out function for query results (see code below function first)
def printOutput(ws_output):
#Loops through a list of dictionary items
index=1
for object in ws_output:
#calls select dictionary keys to print out values
print_output = ' '+str(index)+')'+'species:'+object['species']+'\t '
print_output+= 'id:'+object['id']+'\t '+'name:'+object['name']
print print_output
index+=1
# Load SOAPpy and dependent modules (fpconst) and access the remote
# SOAP server through a proxy class, SOAPProxy - see:
# (http://diveintopython.org/soap_web_services/first_steps.html)
from SOAPpy import SOAPProxy
url = 'http://www.wikipathways.org/wpi/webservice/webservice.php'
namespace = 'http://www.wikipathways.org/webservice'
server = SOAPProxy(url, namespace)
# Define the order of args: needed for this service
server.config.argsOrdering = {'findPathwaysByXref': ('ids', 'codes') }
# findPathwaysByXref (multiple args; returns list of dictionary references)
sc = 'S'; gi = 'P00488'
probeset_containing = server.findPathwaysByXref(codes=sc, ids=gi )
print '\nPathways containing the gene ID "%s" for system code "%s"' % (gi,sc)
printOutput(probeset_containing)
