def test_pca_bigwig_gene_density_intermediate_matrices_norm():
pca1 = NamedTemporaryFile(suffix='.bw', delete=False)
pca2 = NamedTemporaryFile(suffix='.bw', delete=False)
pearson_matrix = NamedTemporaryFile(suffix='.cool', delete=False)
obs_exp_matrix = NamedTemporaryFile(suffix='.cool', delete=False)
pca1.close()
pca2.close()
pearson_matrix.close()
obs_exp_matrix.close()
matrix = ROOT + "small_test_matrix.h5"
gene_track = ROOT + 'dm3_genes.bed.gz'
chromosomes = 'chrX chrXHet'
args = "--matrix {} --outputFileName {} {} -f bigwig -noe 2 \
--extraTrack {} --chromosomes {} --pearsonMatrix {} --obsexpMatrix {}\
--norm".format(matrix, pca1.name, pca2.name, gene_track, chromosomes,
pearson_matrix.name, obs_exp_matrix.name).split()
hicPCA.main(args)
chrom_list = ['chrX', 'chrXHet']
assert are_files_equal_bigwig(ROOT + "hicPCA/pca1_gene_track.bw",
pca1.name, chrom_list)
assert are_files_equal_bigwig(ROOT + "hicPCA/pca2_gene_track.bw",
pca2.name, chrom_list)
test_pearson = hm.hiCMatrix(ROOT + "hicPCA/pearson_norm.cool")
new_pearson = hm.hiCMatrix(pearson_matrix.name)
test_obs_exp = hm.hiCMatrix(ROOT + "hicPCA/obsexp_norm.cool")
new_obs_exp = hm.hiCMatrix(obs_exp_matrix.name)
# load h5 matrices to compare if they are store the same data
test_obs_exp_h5 = hm.hiCMatrix(ROOT + "hicPCA/obsexp_norm.h5")
test_pearson_h5 = hm.hiCMatrix(ROOT + "hicPCA/pearson_norm.h5")
nt.assert_array_almost_equal(test_pearson.matrix.data,
new_pearson.matrix.data,
decimal=DELTA_DECIMAL)
nt.assert_array_almost_equal(test_obs_exp.matrix.data,
new_obs_exp.matrix.data,
decimal=DELTA_DECIMAL)
nt.assert_array_almost_equal(test_pearson_h5.matrix.data,
new_pearson.matrix.data,
decimal=DELTA_DECIMAL)
nt.assert_array_almost_equal(test_obs_exp_h5.matrix.data,
new_obs_exp.matrix.data,
decimal=DELTA_DECIMAL)
os.unlink(pca1.name)
os.unlink(pca2.name)
os.unlink(obs_exp_matrix.name)
os.unlink(pearson_matrix.name)
def test_pca_bedgraph_ignore_masked_bins():
pca1 = NamedTemporaryFile(suffix='.bedgraph', delete=False)
pca2 = NamedTemporaryFile(suffix='.bedgraph', delete=False)
pca1.close()
pca2.close()
matrix = ROOT + "small_test_matrix_50kb_res.h5"
args = "--matrix {} --outputFileName {} {} -f bedgraph -noe 2 --ignoreMaskedBins"\
.format(matrix, pca1.name, pca2.name).split()
hicPCA.main(args)
assert are_files_equal(ROOT + "hicPCA/pca1_ignoredMaskedBins.bedgraph", pca1.name)
assert are_files_equal(ROOT + "hicPCA/pca2_ignoredMaskedBins.bedgraph", pca2.name)
os.unlink(pca1.name)
os.unlink(pca2.name)
def test_pca_bigwig():
pca1 = NamedTemporaryFile(suffix='.bw', delete=False)
pca2 = NamedTemporaryFile(suffix='.bw', delete=False)
pca1.close()
pca2.close()
matrix = ROOT + "small_test_matrix_50kb_res.h5"
args = "--matrix {} --outputFileName {} {} -f bigwig -noe 2".format(
matrix, pca1.name, pca2.name).split()
hicPCA.main(args)
assert are_files_equal_bigwig(ROOT + "hicPCA/pca1.bw", pca1.name)
assert are_files_equal_bigwig(ROOT + "hicPCA/pca2.bw", pca2.name)
os.unlink(pca1.name)
os.unlink(pca2.name)
def test_pca_bedgraph_lieberman():
pca1 = NamedTemporaryFile(suffix='.bedgraph', delete=False)
pca2 = NamedTemporaryFile(suffix='.bedgraph', delete=False)
pca1.close()
pca2.close()
matrix = ROOT + "small_test_matrix_50kb_res.h5"
args = "--matrix {} --outputFileName {} {} -f bedgraph --whichEigenvectors 1 2 --method lieberman"\
.format(matrix, pca1.name, pca2.name).split()
hicPCA.main(args)
# compute(hicPCA.main, args, 5)
assert are_files_equal(ROOT + "hicPCA/pca1.bedgraph", pca1.name)
assert are_files_equal(ROOT + "hicPCA/pca2.bedgraph", pca2.name)
os.unlink(pca1.name)
os.unlink(pca2.name)
def test_pca_bedgraph_gene_density():
pca1 = NamedTemporaryFile(suffix='.bedgraph', delete=False)
pca2 = NamedTemporaryFile(suffix='.bedgraph', delete=False)
pca1.close()
pca2.close()
matrix = ROOT + "small_test_matrix.h5"
gene_track = ROOT + 'dm3_genes.bed.gz'
chromosomes = 'chrX chrXHet'
args = "--matrix {} --outputFileName {} {} -f bedgraph -noe 2 --geneTrack {} --chromosomes {}".format(
matrix, pca1.name, pca2.name, gene_track, chromosomes).split()
hicPCA.main(args)
assert are_files_equal(ROOT + "hicPCA/pca1_gene_track.bedgraph", pca1.name)
assert are_files_equal(ROOT + "hicPCA/pca2_gene_track.bedgraph", pca2.name)
os.unlink(pca1.name)
os.unlink(pca2.name)
def test_pca_bedgraph_histoneMark_track():
pca1 = NamedTemporaryFile(suffix='.bedgraph', delete=False)
pca2 = NamedTemporaryFile(suffix='.bedgraph', delete=False)
pca1.close()
pca2.close()
matrix = ROOT + "small_test_matrix.h5"
extra_track = ROOT + 'bigwig_chrx_2e6_5e6.bw'
chromosomes = 'chrX '
args = "--matrix {} --outputFileName {} {} -f bedgraph -noe 2 \
--extraTrack {} --chromosomes {}"\
.format(matrix, pca1.name, pca2.name, extra_track, chromosomes).split()
hicPCA.main(args)
assert are_files_equal(ROOT + "hicPCA/pca1_chip_track.bedgraph",
pca1.name)
assert are_files_equal(ROOT + "hicPCA/pca2_chip_track.bedgraph",
pca2.name)
os.unlink(pca1.name)
os.unlink(pca2.name)
def test_pca_bigwig():
pca1 = NamedTemporaryFile(suffix='.bw', delete=False)
pca2 = NamedTemporaryFile(suffix='.bw', delete=False)
pca1.close()
pca2.close()
matrix = ROOT + "small_test_matrix_50kb_res.h5"
args = "--matrix {} --outputFileName {} {} -f bigwig -noe 2"\
.format(matrix, pca1.name, pca2.name).split()
hicPCA.main(args)
chrom_list = ['chr2L', 'chr2R', 'chr3L', 'chr3R', 'chr2RHet',
'chr3RHet', 'chr2LHet', 'chr4', 'chrU', 'chrX',
'chrXHet', 'chr3LHet']
assert are_files_equal_bigwig(ROOT + "hicPCA/pca1.bw",
pca1.name, chrom_list)
assert are_files_equal_bigwig(ROOT + "hicPCA/pca2.bw",
pca2.name, chrom_list)
os.unlink(pca1.name)
os.unlink(pca2.name)
def test_pca_bigwig_gene_density():
pca1 = NamedTemporaryFile(suffix='.bw', delete=False)
pca2 = NamedTemporaryFile(suffix='.bw', delete=False)
pca1.close()
pca2.close()
matrix = ROOT + "small_test_matrix.h5"
gene_track = ROOT + 'dm3_genes.bed.gz'
chromosomes = 'chrX chrXHet'
args = "--matrix {} --outputFileName {} {} -f bigwig -noe 2 \
--extraTrack {} --chromosomes {}"\
.format(matrix, pca1.name, pca2.name, gene_track, chromosomes).split()
hicPCA.main(args)
chrom_list = ['chrX', 'chrXHet']
assert are_files_equal_bigwig(ROOT + "hicPCA/pca1_gene_track.bw",
pca1.name, chrom_list)
assert are_files_equal_bigwig(ROOT + "hicPCA/pca2_gene_track.bw",
pca2.name, chrom_list)
os.unlink(pca1.name)
os.unlink(pca2.name)
