def loadData(bfile,
extractSim,
phenoFile,
missingPhenotype='-9',
loadSNPs=False,
standardize=True):
bed = Bed(bfile)
if (extractSim is not None):
f = open(extractSim)
csvReader = csv.reader(f)
extractSnpsSet = set([])
for l in csvReader:
extractSnpsSet.add(l[0])
f.close()
keepSnpsInds = [
i for i in xrange(bed.sid.shape[0]) if bed.sid[i] in extractSnpsSet
]
bed = bed[:, keepSnpsInds]
phe = None
if (phenoFile is not None):
bed, phe = loadPheno(bed, phenoFile, missingPhenotype)
if (loadSNPs):
bed = bed.read()
if (standardize): bed = bed.standardize()
return bed, phe
def loadData(bfile, extractSim, phenoFile, missingPhenotype='-9', loadSNPs=False, standardize=True): bed = Bed(bfile) if (extractSim is not None): f = open(extractSim) csvReader = csv.reader(f) extractSnpsSet = set([]) for l in csvReader: extractSnpsSet.add(l[0]) f.close() keepSnpsInds = [i for i in xrange(bed.sid.shape[0]) if bed.sid[i] in extractSnpsSet] bed = bed[:, keepSnpsInds] phe = None if (phenoFile is not None): bed, phe = loadPheno(bed, phenoFile, missingPhenotype) if (loadSNPs): bed = bed.read() if (standardize): bed = bed.standardize() return bed, phe
