def test_makes_df_ctrl(self):
# This takes about 20min on v1/v2
from idiva.clf.df import v0_df
from idiva.io import ReadVCF
with download(URLS['ctrl']).now.open(mode='rb') as fd:
with open_maybe_gz(fd) as fd:
assert isinstance(fd, io.TextIOBase)
df = v0_df(ReadVCF(fd))
self.assertTrue(len(df) > 0)
self.assertEqual(len(df), ref_len_v2['ctrl'])
def test_combines(self):
from idiva.io import ReadVCF
from idiva.clf.df import v0_df, join
dfs = {}
for k in URLS:
with download(URLS[k]).now.open(mode='rb') as fd:
with open_maybe_gz(fd) as fd:
assert isinstance(fd, io.TextIOBase)
dfs[k] = v0_df(ReadVCF(fd))
df = join(case=dfs['case'], ctrl=dfs['ctrl'])
def test_join_does_something(self):
from idiva.io import ReadVCF
from idiva.clf.df import v0_df, join
dfs = {}
for k in PATHS:
with PATHS[k].open(mode='r') as fd:
assert isinstance(fd, io.TextIOBase)
dfs[k] = v0_df(ReadVCF(fd))
df = join(case=dfs['case'], ctrl=dfs['ctrl'])
def test_makes_df(self):
from idiva.clf.df import v0_df
from idiva.io import ReadVCF
from idiva.utils import seek_then_rewind
for k in PATHS:
with PATHS[k].open(mode='r') as fd:
assert isinstance(fd, io.TextIOBase)
with seek_then_rewind(fd):
datalines = list(ReadVCF(fd))
with seek_then_rewind(fd):
df = v0_df(ReadVCF(fd))
self.assertEqual(len(datalines), len(df))
def test_chi2_large_head(self):
from idiva.io import ReadVCF, open_maybe_gz
from idiva.clf.df import v0_df, join
dfs = {}
for (k, file) in PATHS_LARGE_HEAD.items():
with open_maybe_gz(file, mode='r') as fd:
dfs[k] = v0_df(ReadVCF(fd))
df = join(case=dfs['case'], ctrl=dfs['ctrl'])
cols = tuple([F"ALT{n}_{kind}" for n in range(3)]
for kind in ['case', 'ctrl'])
pp = chi2_test(df[cols[0] + cols[1]], cols, add=1)
def test_chi2_large(self):
from idiva.io import ReadVCF, open_maybe_gz
from idiva.clf.df import v0_df, join
dfs = {}
for k in URLS_LARGE:
with download(URLS_LARGE[k]).now.open(mode='rb') as fd:
with open_maybe_gz(fd, mode='r') as fd:
dfs[k] = v0_df(ReadVCF(fd))
df = join(case=dfs['case'], ctrl=dfs['ctrl'])
cols = tuple([F"ALT{n}_{kind}" for n in range(3)]
for kind in ['case', 'ctrl'])
p = chi2_test(df[cols[0] + cols[1]], cols, add=1)
def test_combine(self):
from idiva.io import ReadVCF
from idiva.io.vcf import SEP
from idiva.clf.df import v0_df, join, dtype_v0
dfs = {}
for k in PATHS:
with PATHS[k].open(mode='r') as fd:
assert isinstance(fd, io.TextIOBase)
dfs[k] = v0_df(ReadVCF(fd))
candidate = join(case=dfs['case'], ctrl=dfs['ctrl'])
def read_csv(file) -> pd.DataFrame:
return pd.read_csv(file, sep=SEP).astype(
{
'CHROM': str,
'POS': int,
'ID': str,
'ALT0_case': float, 'ALT1_case': float, 'ALT2_case': float,
'ALT0_ctrl': float, 'ALT1_ctrl': float, 'ALT2_ctrl': float,
}
)
ref_file = MY_SPACE / "reference.txt"
# Hack to create the reference
# candidate.to_csv(ref_file, sep=SEP, index=True)
reference = read_csv(ref_file)
# Write and read `candidate` to make comparable to `reference`
import tempfile
with tempfile.NamedTemporaryFile(mode='w') as tf:
candidate.to_csv(tf, sep=SEP, index=True)
tf.flush()
candidate = read_csv(tf.name)
self.assertTrue(reference.equals(candidate))
def df_maker1():
# Note: v0_df is parallelized
return join(case=v0_df(case), ctrl=v0_df(ctrl))