def importMarkerFinderHits(fn):
genes = {}
ICGS_State_ranked = {}
skip = True
for line in open(fn, 'rU').xreadlines():
data = clustering.cleanUpLine(line)
if skip: skip = False
else:
try:
gene, symbol, rho, ICGS_State = string.split(data, '\t')
except Exception:
gene, symbol, rho, rho_p, ICGS_State = string.split(
data, '\t')
#if ICGS_State!=state and float(rho)>0.0:
if float(rho) > 0.15:
try:
ICGS_State_ranked[ICGS_State].append(
[float(rho), gene, symbol])
except Exception:
ICGS_State_ranked[ICGS_State] = [[
float(rho), gene, symbol
]]
for ICGS_State in ICGS_State_ranked:
ICGS_State_ranked[ICGS_State].sort()
ICGS_State_ranked[ICGS_State].reverse()
#print ICGS_State, ICGS_State_ranked[ICGS_State][:50]
for (rho, gene, symbol) in ICGS_State_ranked[ICGS_State][:50]:
genes[
gene] = rho, ICGS_State ### Retain all population specific genes (lax)
genes[symbol] = rho, ICGS_State
return genes
def importGeneLists(fn):
genes = {}
for line in open(fn, 'rU').xreadlines():
data = clustering.cleanUpLine(line)
gene, cluster = string.split(data, '\t')[0:2]
genes[gene] = cluster
return genes