print " --> number of samples : ", numSamples
# if the user wants to use the "adjP" option, then we set the p-value based on
# the number of samples ... right now the approach is to do 1.e-X where X=5+(N/100)
# and N is the number of samples
if (args.adjP):
args.pvalue = (1. / 100000.) / float(10.**(int(numSamples / 100)))
print " --> setting pvalue threshold to : ", args.pvalue
# we need to pre-process the tsv file (unless it appears to have already
# been done)
binFile = preProcessTSV(tsvFile)
# create a random name for this particular run ...
# and then make a subdirectory for the outputs ...
curJobName = miscIO.make_random_fname()
print " "
print " randomly generated job name : <%s> " % curJobName
print " "
tmpDir = "%s/%s" % (gidgetConfigVars['TCGAFMP_CLUSTER_SCRATCH'],
curJobName)
cmdString = "mkdir %s" % tmpDir
(status, output) = commands.getstatusoutput(cmdString)
if (not os.path.exists(tmpDir)):
print " mkdir command failed ??? "
print cmdString
sys.exit(-1)
# open the jobInfo file ...
jobFile = tmpDir + "/jobInfo.txt"
index = int(args.one)
except:
index = getFeatureIndex(args.one, args.tsvFile)
iRanges2 = [ ( index, index ) ]
print " single index range : ", iRanges2
# if the user wants to use the "adjP" option, then we set the p-value based on
# the number of samples ... right now the approach is to do 1.e-X where X=5+(N/100)
# and N is the number of samples
if (args.adjP):
args.pvalue = (1. / 100000.) / float(10. ** (int(numSamples / 100)))
print " --> setting pvalue threshold to : ", args.pvalue
# create a random name for this particular run ...
# and then make a subdirectory for the outputs ...
curJobName = miscIO.make_random_fname()
print " "
print " randomly generated job name : <%s> " % curJobName
print " "
tmpDir13 = "%s/%s" % (gidgetConfigVars['TCGAFMP_CLUSTER_SCRATCH'], curJobName)
cmdString = "mkdir %s" % tmpDir13
(status, output) = commands.getstatusoutput(cmdString)
if (not os.path.exists(tmpDir13)):
print " mkdir command failed ??? "
print cmdString
sys.exit(-1)
# open the jobInfo file ...
jobFile = tmpDir13 + "/jobInfo.txt"
try: