featureFile = args[1]
iplMatrix = None
global verbose, globalList, globalPathway
for o, a in opts:
if o == "-q":
verbose = False
elif o == "-i":
iplMatrix = a
## build sourceList
typeFile = "/".join(re.split("/", sifFile)[:-2] + ["TYPE.NA"])
sourceList = re.split("/", sifFile)[-2] + ".list_t"
h = mData.rList(featureFile)
(n, i) = mPathway.rSIF(sifFile, typef=typeFile)
(gn, gi) = mPathway.rPathway(globalPathway)
p = mPathway.Pathway(n, i)
s = mPathway.sortConnected(p)
f = open(sourceList, "w")
c = 1
for i in s:
u = list(set(i) & set(h))
if len(u) >= 5:
f.write("component_%s\t%s\n" % (c, "\t".join(u)))
c += 1
break
f.write("component_all\t%s\n" % ("\t".join(list(set(n.keys()) & set(h)))))
f.write("all\t%s\n" % ("\t".join(list(set(gn.keys()) & set(h)))))
f.close()
featureFile = args[1]
iplMatrix = None
global verbose, globalList, globalPathway
for o, a in opts:
if o == "-q":
verbose = False
elif o == "-i":
iplMatrix = a
## build sourceList
typeFile = "/".join(re.split("/", sifFile)[:-2] + ["TYPE.NA"])
sourceList = re.split("/", sifFile)[-2] + ".list_t"
h = mData.rList(featureFile)
(n, i) = mPathway.rSIF(sifFile, typef=typeFile)
(gn, gi) = mPathway.rPathway(globalPathway)
p = mPathway.Pathway(n, i)
s = mPathway.sortConnected(p)
f = open(sourceList, "w")
c = 1
for i in s:
u = list(set(i) & set(h))
if len(u) >= 5:
f.write("component_%s\t%s\n" % (c, "\t".join(u)))
c += 1
break
f.write("component_all\t%s\n" % ("\t".join(list(set(n.keys()) & set(h)))))
f.write("all\t%s\n" % ("\t".join(list(set(gn.keys()) & set(h)))))
f.close()
assert os.path.exists("TYPE.NA")
assert os.path.exists("%s_SCORE.NA" % (feature))
assert os.path.exists("%s" % (feature))
if feature.startswith("disc-plot"):
mutTable = True
mutGene = re.sub("disc-plot", "", feature)
if os.path.exists("%s/img" % (feature)):
customImage = True
## identify nets with feature
sifFile = None
for i in os.listdir("%s" % (feature+"/")):
if i.endswith(netExtension):
sifFile = feature+"/"+i
break
(allNodes, allInteractions) = mPathway.rSIF(sifFile)
idMap = dict()
nodeMap = dict()
for i, node in enumerate(allNodes.keys()):
idMap[node] = i+1
nodeMap[i+1] = node
labelMap = mData.r2Col("LABEL.NA", delim = " = ", header = True)
typeMap = mData.r2Col("TYPE.NA", delim = " = ", header = True)
scoreMap = mData.r2Col("%s_SCORE.NA" % (feature), delim = " = ", header = True)
nodes = nodeMap.keys()
nodes.sort()
## create graphml structure
graphmlContent = """<graphml>\\
<key id="name" for="node" attr.name="name" attr.type="string"/>\\
<key id="label" for="node" attr.name="label" attr.type="string"/>\\
assert os.path.exists("TYPE.NA")
assert os.path.exists("%s_SCORE.NA" % (feature))
assert os.path.exists("%s" % (feature))
if feature.startswith("disc-plot"):
mutTable = True
mutGene = re.sub("disc-plot", "", feature)
if os.path.exists("%s/img" % (feature)):
customImage = True
## identify nets with feature
sifFile = None
for i in os.listdir("%s" % (feature + "/")):
if i.endswith(netExtension):
sifFile = feature + "/" + i
break
(allNodes, allInteractions) = mPathway.rSIF(sifFile)
idMap = dict()
nodeMap = dict()
for i, node in enumerate(allNodes.keys()):
idMap[node] = i + 1
nodeMap[i + 1] = node
labelMap = mData.r2Col("LABEL.NA", delim=" = ", header=True)
typeMap = mData.r2Col("TYPE.NA", delim=" = ", header=True)
scoreMap = mData.r2Col("%s_SCORE.NA" % (feature), delim=" = ", header=True)
nodes = nodeMap.keys()
nodes.sort()
## create graphml structure
graphmlContent = """<graphml>\\
<key id="name" for="node" attr.name="name" attr.type="string"/>\\
<key id="label" for="node" attr.name="label" attr.type="string"/>\\