def run():
if settings.input_format != 'plink':
inp = open(settings.infile) if not settings.input_format == 'gzip' else gzip.open(settings.infile)
line = inp.readline()
orig_values = [float(value) for value in line.split()]
if not settings.permutations:
settings.permutations = sum(1 for _ in inp)
inp.close()
landscape = get_landscape(orig_values)
landscape_generator = landscape_generator_file()
else:
inds, snps, genos = plink.read_plink(settings.infile)
orig_values = plink.assoc(inds, genos)
landscape = get_landscape(orig_values)
landscape_generator = landscape_generator_plink()
if settings.permutations > 0:
if settings.score_evaluation == 'A1':
pvalues, EM = get_pvalues_A1(landscape, landscape_generator)
elif settings.score_evaluation == 'A2':
pvalues, EM = get_pvalues_A2(landscape, landscape_generator)
else:
pvalues = get_pvalues_A0(landscape)
EM = len(pvalues)
else:
pvalues = [1 for _ in landscape.maximal_segments]
EM = 1
write_results(landscape, pvalues, EM, settings)
write_ak_text(orig_values, landscape, settings)
def landscape_generator_plink():
inds, snps, genos = plink.read_plink(settings.infile)
random.seed(settings.random_seed)
while 1:
inds.pheno = np.random.permutation(inds.pheno)
pvals = plink.assoc(inds, genos)
yield get_landscape(pvals)