def test_merge_chrom(self):
s1 = SNPs("tests/input/generic.csv")
df = s1.snps.append(
self.create_snp_df(
rsid=["rs100", "rs101", "rs102", "rs103"],
chrom=["Y", "Y", "Y", "Y"],
pos=[100, 101, 102, 103],
genotype=["A", np.nan, "A", "A"],
))
s1._snps = df.copy()
s2 = SNPs()
s2._build = 37
s2._snps = df.copy()
# set values for chrom that will be ignored (that would otherwise result in
# identification of discrepant SNPs or updating genotype)
s2._snps.loc["rs3", "pos"] = 1003 # discrepant position
s2._snps.loc["rs4", "genotype"] = "AA" # discrepant genotype
s2._snps.loc["rs5", "genotype"] = "AA"
# set values for chrom to be merged
s2._snps.loc["rs100", "genotype"] = "T" # discrepant genotype
s2._snps.loc["rs101", "genotype"] = "A"
s2._snps.loc["rs102", "pos"] = 1002 # discrepant position
# set expected values for merge result
df.loc["rs100",
"genotype"] = np.nan # discrepant genotype sets to np.nan
df.loc["rs101", "genotype"] = "A" # updates np.nan
results = s1.merge([s2], chrom="Y")
pd.testing.assert_frame_equal(s1.snps, df, check_exact=True)
self.assert_results(
results,
[{
"merged":
True,
"common_rsids":
pd.Index(["rs100", "rs101", "rs102", "rs103"], name="rsid"),
"discrepant_position_rsids":
pd.Index(["rs102"], name="rsid"),
"discrepant_genotype_rsids":
pd.Index(["rs100"], name="rsid"),
}],
)
self.assertEqual(len(s1.discrepant_merge_positions), 1)
self.assertEqual(len(s1.discrepant_merge_genotypes), 1)
def simulate_snps(
self,
chrom="1",
pos_start=1,
pos_max=248140902,
pos_step=100,
genotype="AA",
insert_nulls=True,
null_snp_step=101,
complement_genotype_one_chrom=False,
complement_genotype_two_chroms=False,
complement_snp_step=50,
):
s = SNPs()
s._build = 37
positions = np.arange(pos_start, pos_max, pos_step, dtype=np.uint32)
snps = pd.DataFrame(
{"chrom": chrom},
index=pd.Index(["rs" + str(x + 1) for x in range(len(positions))],
name="rsid"),
)
snps["pos"] = positions
snps["genotype"] = genotype
if insert_nulls:
snps.loc[snps.iloc[0::null_snp_step, :].index, "genotype"] = np.nan
indices = snps.iloc[0::complement_snp_step, :].index
if complement_genotype_two_chroms:
snps.loc[indices,
"genotype"] = snps.loc[indices, "genotype"].apply(
self.complement_two_chroms)
elif complement_genotype_one_chrom:
snps.loc[indices,
"genotype"] = snps.loc[indices, "genotype"].apply(
self.complement_one_chrom)
s._snps = snps
return s