def __init__(self, forcedUpdate=False, organismCode="HSA"):
"""Initialization. HSA is the organism code for human."""
self.update(forced=forcedUpdate)
self.net = MetabolicNetwork()
self.organismCode = organismCode
class KEGG:
rawDataFiles = {'compound': 'ftp://ftp.genome.jp/pub/kegg/ligand/compound/compound',
'enzyme': 'ftp://ftp.genome.jp/pub/kegg/ligand/enzyme/enzyme'}
def __init__(self, forcedUpdate=False, organismCode="HSA"):
"""Initialization. HSA is the organism code for human."""
self.update(forced=forcedUpdate)
self.net = MetabolicNetwork()
self.organismCode = organismCode
def update(self, forced=False):
"""update data files. The default directory is data/."""
if forced:
self.retrieveFiles(self.rawDataFiles.keys())
else:
dataFiles = os.listdir('data/')
toBeUpdated = filter(lambda x: x not in dataFiles, self.rawDataFiles.keys())
self.retrieveFiles(toBeUpdated)
def retrieveFiles(self, files):
"""retrieve files from KEGG database."""
if len(files) == 0:
print "There is no file to be updated."
else:
print "updating following files:", ','.join(files)
for f in files:
print "downloading %s..." % (f)
urllib.urlretrieve(self.rawDataFiles[f], 'data/' + f)
def writeNet(self):
self.net.writeNet()
def constructNetwork(self):
"""docstring for constructNetwork"""
self.parseEnzyme(organismCode=self.organismCode)
self.parseCompound()
self.net.connectNodes()
def parseEnzyme(self, filename="data/enzyme", organismCode="HSA"):
print "parsing the enzyme list..."
entries = open(filename).read().split('///')
for aEntry in entries:
enzyme = Enzyme()
organismFlag = 0
for line in aEntry.split('\n'):
temp = line[:12].strip()
context = temp if temp != '' else context
data = line[12:].strip()
if context == "ENTRY":
enzyme.entry = data.split()[1]
elif context == "NAME":
enzyme.names.append(data.strip(';'))
elif context == "CLASS":
enzyme.classes.append(data.strip(';'))
elif context in ["SUBSTRATE", "PRODUCT", "COFACTOR"]:
try:
enzyme.compounds.append(data.split(':')[1].strip('];'))
except IndexError:
continue
elif context == "PATHWAY":
try:
enzyme.pathways.append(data.split(':')[1].split(' '))
except IndexError:
enzyme.pathways.append(('', data.strip()))
elif context == "GENES":
if organismCode in data: organismFlag = 1
else:
continue
if not organismFlag:
continue
else:
self.net.addNode(enzyme)
def parseCompound(self, filename="data/compound"):
"""docstring for parseCompound"""
print "parsing the compound list..."
entries = open(filename).read().split('///')
for aEntry in entries:
compound = Compound()
for line in aEntry.split('\n'):
temp = line[:12].strip()
context = temp if temp != '' else context
data = line[12:].strip()
if context == "ENTRY":
compound.entry = data.split()[0]
elif context == "NAME":
compound.names.append(data.strip(';'))
elif context == "REACTION":
[compound.reactions.append(r) for r in data.split()]
elif context == "PATHWAY":
try:
compound.pathways.append(data.split(':')[1].split(' '))
except:
compound.pathways.append(('', data.strip()))
elif context == "ENZYME":
[compound.enzymes.append(e) for e in data.split()]
else:
continue
self.net.addNode(compound)