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import os
import sys
import numpy
import pytest
try:
sys.path.insert(0, os.path.dirname(os.path.dirname(__file__)))
except Exception:
sys.path.insert(0, os.path.dirname(os.path.abspath(".")))
from bx.bbi.bigwig_file import BigWigFile
def allclose(a, b, tol=0.00001):
"""
Like numpy.allclose but treat Nan == Nan
"""
d = numpy.absolute(a - b)
return numpy.all(numpy.isnan(d) | (d < tol))
class TestBigWig:
@pytest.fixture(autouse=True)
def setUp(self):
f = open("test_data/bbi_tests/test.bw", "rb")
self.bw = BigWigFile(file=f)
def test_get_summary(self):
data = self.bw.query("chr1", 10000, 20000, 10)
means = [x["mean"] for x in data]
assert numpy.allclose(
[float(_) for _ in means],
[
-0.17557571594973645,
-0.054009292602539061,
-0.056892242431640622,
-0.03650328826904297,
0.036112907409667966,
0.0064466032981872557,
0.036949024200439454,
0.076638259887695306,
0.043518108367919923,
0.01554749584197998,
],
)
# Summarize variant
sd = self.bw.summarize("chr1", 10000, 20000, 10)
assert numpy.allclose(
sd.sum_data / sd.valid_count,
[
-0.17557571594973645,
-0.054009292602539061,
-0.056892242431640622,
-0.03650328826904297,
0.036112907409667966,
0.0064466032981872557,
0.036949024200439454,
0.076638259887695306,
0.043518108367919923,
0.01554749584197998,
],
)
# Test min and max for this entire summary region
data = self.bw.query("chr1", 10000, 20000, 1)
maxs = [x["max"] for x in data]
mins = [x["min"] for x in data]
assert [float(_) for _ in maxs] == [0.289000004529953]
assert [float(_) for _ in mins] == [-3.9100000858306885]
def test_get_leaf(self):
data = self.bw.query("chr1", 11000, 11005, 5)
means = [x["mean"] for x in data]
assert numpy.allclose(
[float(_) for _ in means],
[
0.050842501223087311,
-2.4589500427246094,
0.050842501223087311,
0.050842501223087311,
0.050842501223087311,
],
)
# Test min and max for this entire leaf region
data = self.bw.query("chr1", 11000, 11005, 1)
maxs = [x["max"] for x in data]
mins = [x["min"] for x in data]
assert [float(_) for _ in maxs] == [0.050842501223087311]
assert [float(_) for _ in mins] == [-2.4589500427246094]
def test_wrong_nochrom(self):
data = self.bw.query("chr2", 0, 10000, 10)
assert data is None
@pytest.mark.parametrize("line", open("test_data/bbi_tests/test.expectation").readlines())
def test_summary_from_file(self, line):
fields = line.split()
chrom = fields[0]
start = int(fields[1])
end = int(fields[2])
n = int(fields[3])
t = fields[4]
values = [float(v.replace("n/a", "NaN")) for v in fields[5:]]
sd = self.bw.summarize(chrom, start, end, n)
if t == "mean":
assert allclose(sd.sum_data / sd.valid_count, values)
elif t == "min":
assert allclose(sd.min_val, values)
elif t == "max":
assert allclose(sd.max_val, values)
# elif t == 'std':
# assert numpy.allclose( sd.max_val, values )
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