def test_correct_matrix_diagnostic_plot():
outfile = NamedTemporaryFile(
suffix='.png', prefix='hicexplorer_test', delete=False)
args = "diagnostic_plot --matrix {} --chromosomes chrUextra chr3LHet " \
" --plotName {}".format(ROOT + "small_test_matrix.h5",
outfile.name).split()
hicCorrectMatrix.main(args)
res = compare_images(ROOT + "hicCorrectMatrix" +
'/diagnostic_plot.png', outfile.name, tol=40)
assert res is None, res
os.remove(outfile.name)
def test_correct_matrix_KR_partial_cool():
outfile = NamedTemporaryFile(suffix='_KR.cool', delete=False)
outfile.close()
args = "correct --matrix {} --correctionMethod KR --chromosomes "\
"chrUextra chr3LHet --outFileName {} ".format(ROOT + "small_test_matrix.cool",
outfile.name).split()
hicCorrectMatrix.main(args)
test = hm.hiCMatrix(ROOT + "hicCorrectMatrix/kr_partial.cool")
new = hm.hiCMatrix(outfile.name)
nt.assert_almost_equal(test.matrix.data, new.matrix.data, decimal=5)
nt.assert_equal(test.cut_intervals, new.cut_intervals)
os.unlink(outfile.name)
def test_correct_matrix():
outfile = NamedTemporaryFile(suffix='.h5', delete=False)
outfile.close()
args = "correct --matrix {} --chromosomes chrUextra chr3LHet --iterNum 500 " \
" --outFileName {} --filterThreshold -1.5 5.0".format(ROOT + "small_test_matrix.h5",
outfile.name).split()
hicCorrectMatrix.main(args)
test = hm.hiCMatrix(
ROOT +
"hicCorrectMatrix/small_test_matrix_corrected_chrUextra_chr3LHet.h5")
new = hm.hiCMatrix(outfile.name)
nt.assert_equal(test.matrix.data, new.matrix.data)
nt.assert_equal(test.cut_intervals, new.cut_intervals)
os.unlink(outfile.name)