def test_na(self):
self.dat.loc[0, 'SNP'] = float('NaN')
self.dat.loc[1, 'A2'] = float('NaN')
self.dat_gen = [
self.dat.loc[0:4, :], self.dat.loc[5:9, :].reset_index(drop=True)]
dat = munge.parse_dat(
self.dat_gen, self.convert_colname, None, log, self.args)
assert_frame_equal(
dat, self.dat.loc[2:, ['SNP', 'A1', 'A2', 'P']].reset_index(drop=True))
def test_merge_alleles(self):
self.args.merge_alleles = True
merge_alleles = pd.DataFrame()
merge_alleles['SNP'] = ['rs' + str(i) for i in range(3)]
merge_alleles['MA'] = ['AG', 'AG', 'AG']
dat = munge.parse_dat(self.dat_gen, self.convert_colname,
merge_alleles, log, self.args)
print self.dat.loc[0:2, ['SNP', 'A1', 'A2', 'P']]
assert_frame_equal(dat, self.dat.loc[0:2, ['SNP', 'A1', 'A2', 'P']])
def test_merge_alleles(self):
self.args.merge_alleles = True
merge_alleles = pd.DataFrame()
merge_alleles['SNP'] = ['rs' + str(i) for i in range(3)]
merge_alleles['MA'] = ['AG', 'AG', 'AG']
dat = munge.parse_dat(
self.dat_gen, self.convert_colname, merge_alleles, log, self.args)
print self.dat.loc[0:2, ['SNP', 'A1', 'A2', 'P']]
assert_frame_equal(dat, self.dat.loc[0:2, ['SNP', 'A1', 'A2', 'P']])
def test_na(self):
self.dat.loc[0, 'SNP'] = float('NaN')
self.dat.loc[1, 'A2'] = float('NaN')
self.dat_gen = [
self.dat.loc[0:4, :], self.dat.loc[5:9, :].reset_index(drop=True)]
dat = munge.parse_dat(
self.dat_gen, self.convert_colname, None, log, self.args)
assert_frame_equal(
dat, self.dat.loc[2:, ['SNP', 'A1', 'A2', 'P']].reset_index(drop=True))
def test_no_alleles(self):
# test that it doesn't crash with no allele columns and the
# --no-alleles flag set
dat = self.dat.drop(['A1', 'A2'], axis=1)
dat_gen = [dat.loc[0:4, :], dat.loc[5:9, :].reset_index(drop=True)]
self.args.no_alleles = True
dat = munge.parse_dat(dat_gen, self.convert_colname, None, log,
self.args)
assert_frame_equal(dat,
self.dat.drop(['INFO', 'FRQ', 'A1', 'A2'], axis=1))
def test_no_alleles(self):
# test that it doesn't crash with no allele columns and the
# --no-alleles flag set
dat = self.dat.drop(['A1', 'A2'], axis=1)
dat_gen = [dat.loc[0:4, :], dat.loc[5:9, :].reset_index(drop=True)]
self.args.no_alleles = True
dat = munge.parse_dat(
dat_gen, self.convert_colname, None, log, self.args)
assert_frame_equal(
dat, self.dat.drop(['INFO', 'FRQ', 'A1', 'A2'], axis=1))
def test_standard(self):
dat = munge.parse_dat(self.dat_gen, self.convert_colname, None, log,
self.args)
assert_frame_equal(dat, self.dat.drop(['INFO', 'FRQ'], axis=1))
def test_standard(self):
dat = munge.parse_dat(
self.dat_gen, self.convert_colname, None, log, self.args)
assert_frame_equal(dat, self.dat.drop(['INFO', 'FRQ'], axis=1))
