def main(args):
# get the names from the .hud file
names = []
with open(os.path.expanduser(args.hud)) as fin_hud:
for line in util.gen_nonempty_stripped_lines(fin_hud):
name, rest = line.split(None, 1)
names.append(name)
# get case and control status from the matpheno file
cases = set()
controls = set()
with open(os.path.expanduser(args.matpheno)) as fin_matpheno:
for line in util.gen_nonempty_stripped_lines(fin_matpheno):
name, classification = line.split(None, 1)
if classification == '1':
cases.add(name)
elif classification == '2':
controls.add(name)
elif classification in ('12', 'null'):
# skip individuals classified like this
pass
else:
msg = 'invalid MAT_pheno classification: ' + classification
raise Exception(msg)
# write the .ind file contents
for name in names:
gender = 'U'
classification = 'Ignore'
if name in cases:
classification = 'Case'
elif name in controls:
classification = 'Control'
row = [name, gender, classification]
print '\t'.join(row)
def main(args):
# get the names from the .hud file
names = []
with open(os.path.expanduser(args.hud)) as fin_hud:
for line in util.gen_nonempty_stripped_lines(fin_hud):
name, rest = line.split(None, 1)
names.append(name)
# open the csv file
with open(os.path.expanduser(args.csv)) as fin_csv:
# start reading the csv file
rows = list(csv.reader(fin_csv))
header, data_rows = rows[0], rows[1:]
# get case and control OTU sets
if args.environment == 'precipitation':
cases, controls = get_precipitation_info(data_rows,
args.precipitation_threshold)
elif args.environment == 'temperature':
cases, controls = get_temperature_info(data_rows,
args.temperature_threshold)
elif args.environment == 'location':
cases, controls = get_location_info(data_rows,
args.control_location)
else:
msg = 'unrecognized environmental variable: ' + args.environment
raise Exception(msg)
# write the .ind file contents
for name in names:
gender = 'U'
classification = 'Ignore'
if name in cases:
classification = 'Case'
elif name in controls:
classification = 'Control'
row = [name, gender, classification]
print '\t'.join(row)
def main(args):
# for each individual get the genotype of each SNP
array_per_individual = []
for line in util.gen_nonempty_stripped_lines(sys.stdin):
name, genotypes = line.split(None, 1)
arr = genotypes.split()
array_per_individual.append(arr)
# for each SNP get the genotype for each individual
array_per_position = zip(*array_per_individual)
for arr in array_per_position:
print ''.join(arr)
def main(args):
line = util.get_first(util.gen_nonempty_stripped_lines(sys.stdin))
otu_name, genotype_string = line.split(None, 1)
genotypes = genotype_string.split()
for i, genotype in enumerate(genotypes):
name = 'SNP_' + str(i)
chromosome = '1'
morgans = '0.0'
bases = i+1
row = [name, chromosome, morgans, bases]
print '\t'.join(str(x) for x in row)
def main():
values = []
for line in util.gen_nonempty_stripped_lines(sys.stdin):
name, gender, status = line.split()
if status == 'Control':
v = '0'
elif status == 'Case':
v = '1'
elif status == 'Ignore':
v = '9'
else:
msg = 'Invalid status: ' + status
raise Exception(msg)
values.append(v)
print ''.join(values)
