def test_remove_triallelic(self):
args = Args()
args.haps = get_file('triallelic_haps.haps')
args.output = get_file('output.haps')
args.maf = 0.05
args.missing = 0.80
args.hwe = .05
args.chi_square = True
filter_haps_file(args)
with open(args.output) as f:
lines = sum(1 for line in f)
assert lines == 1
os.remove(args.output)
def test_remove_triallelic(self):
args = Args()
args.haps = get_file('triallelic_haps.haps')
args.output = get_file('output.haps')
args.maf = 0.05
args.missing = 0.80
args.hwe = .05
args.chi_square = True
filter_haps_file(args)
with open(args.output) as f:
lines = sum(1 for line in f)
assert lines == 1
os.remove(args.output)
def test_filter_hap_file(self):
args = Args()
args.haps = get_file('filter.haps')
args.output = get_file('output.haps')
args.maf = 0.05
args.missing = 0.05
args.hwe = .05
args.chi_square = True
filter_haps_file(args)
with open(args.output) as f:
lines = sum(1 for line in f)
assert lines == 1
with open(args.output) as f:
line = f.readline()
line = line.split()
assert line[0] == '2'
assert line[1] == 'rs4662641'
assert line[2] == '130000272'
os.remove(args.output)
def test_filter_hap_file(self):
args = Args()
args.haps = get_file('filter.haps')
args.output = get_file('output.haps')
args.maf = 0.05
args.missing = 0.05
args.hwe = .05
args.chi_square = True
filter_haps_file(args)
with open(args.output) as f:
lines = sum(1 for line in f)
assert lines == 1
with open(args.output) as f:
line = f.readline()
line = line.split()
assert line[0] == '2'
assert line[1] == 'rs4662641'
assert line[2] == '130000272'
os.remove(args.output)
