def test_correct_matrix_ICE():
outfile = NamedTemporaryFile(suffix='.ICE.h5', delete=False)
outfile.close()
args = "correct --matrix {} --correctionMethod ICE --chromosomes "\
"chrUextra chr3LHet --iterNum 500 --outFileName {} "\
"--filterThreshold -1.5 5.0".format(ROOT + "small_test_matrix.h5",
outfile.name).split()
# hicCorrectMatrix.main(args)
compute(hicCorrectMatrix.main, args, 5)
test = hm.hiCMatrix(
ROOT + "hicCorrectMatrix/small_test_matrix_ICEcorrected_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)
def test_trivial_functionality(
matrices,
outputFormat,
resolutions,
):
"""
Test for all commandline arguments.
Options for cool input format are testet seperately.
"""
from pathlib import Path
# get suffix of input matrix without the dot
inputFormat = Path(matrices).suffix[1:]
# create file corresponding to output format
outFileName = NamedTemporaryFile(suffix=".{}".format(outputFormat),
delete=True)
outFileName.close()
args = "--matrices {} --outFileName {} --inputFormat {} --outputFormat {} {}".format(
matrices,
outFileName.name,
inputFormat,
outputFormat,
resolutions,
).split()
hicConvertFormat.main(args)
test = hm.hiCMatrix(matrices)
new = hm.hiCMatrix(outFileName.name)
nt.assert_array_almost_equal(test.matrix.data,
new.matrix.data,
decimal=DELTA_DECIMAL)
nt.assert_equal(len(new.cut_intervals), len(test.cut_intervals))
cut_interval_new_ = []
cut_interval_test_ = []
for x in new.cut_intervals:
cut_interval_new_.append(x[:3])
for x in test.cut_intervals:
cut_interval_test_.append(x[:3])
nt.assert_equal(cut_interval_new_, cut_interval_test_)
os.unlink(outFileName.name)
def test_pca_bigwig_gene_density_intermediate_matrices():
pca1 = NamedTemporaryFile(suffix='.bw', delete=False)
pca2 = NamedTemporaryFile(suffix='.bw', delete=False)
pearson_matrix = NamedTemporaryFile(suffix='.h5', delete=False)
obs_exp_matrix = NamedTemporaryFile(suffix='.h5', 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 {}"\
.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_intermediate.h5")
new_pearson = hm.hiCMatrix(pearson_matrix.name)
test_obs_exp = hm.hiCMatrix(ROOT + "hicPCA/obs_exp_intermediate.h5")
new_obs_exp = hm.hiCMatrix(obs_exp_matrix.name)
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)
# assert are_files_equal_bigwig(ROOT + "hicPCA/pearson_intermediate.h5", pearson_matrix.name, chrom_list)
# assert are_files_equal_bigwig(ROOT + "hicPCA/obs_exp_intermediate.h5", obs_exp_matrix.name, chrom_list)
os.unlink(pca1.name)
os.unlink(pca2.name)
os.unlink(obs_exp_matrix.name)
os.unlink(pearson_matrix.name)
def test_correct_matrix_KR():
outfile = NamedTemporaryFile(suffix='.KR.h5', delete=False)
outfile.close()
args = "correct --matrix {} --correctionMethod KR --chromosomes "\
"chrUextra chr3LHet --outFileName {} ".format(ROOT + "small_"
"test_matrix.h5",
outfile.name).split()
hicCorrectMatrix.main(args)
test = hm.hiCMatrix(
ROOT +
"hicCorrectMatrix/small_test_matrix_KRcorrected_chrUextra_chr3LHet.h5")
new = hm.hiCMatrix(outfile.name)
nt.assert_almost_equal(test.matrix.data, new.matrix.data, decimal=10)
nt.assert_equal(test.cut_intervals, new.cut_intervals)
os.unlink(outfile.name)
def test_correct_matrix_KR_cool():
outfile = NamedTemporaryFile(suffix='_KR.cool', delete=False)
outfile.close()
args = "correct --matrix {} --correctionMethod KR "\
"--outFileName {} ".format(ROOT + "small_test_matrix.cool",
outfile.name).split()
# hicCorrectMatrix.main(args)
compute(hicCorrectMatrix.main, args, 5)
test = hm.hiCMatrix(ROOT + "hicCorrectMatrix/kr_full.cool")
new = hm.hiCMatrix(outfile.name)
nt.assert_almost_equal(test.matrix.data, new.matrix.data, decimal=5)
# nt.assert_almost_equal(test.correction_factors, new.correction_factors, decimal=5)
nt.assert_equal(test.cut_intervals, new.cut_intervals)
os.unlink(outfile.name)
def main(args=None):
"""
Main function to generate the polarization plot.
"""
args = parse_arguments().parse_args(args)
matplotlib.rcParams['pdf.fonttype'] = 42
pc1 = pd.read_table(args.pca,
header=None,
sep="\t",
dtype={
0: "object",
1: "Int64",
2: "Int64",
3: "float32"
})
pc1 = pc1.rename(columns={0: "chr", 1: "start", 2: "end", 3: "pc1"})
if args.outliers != 0:
quantile = [args.outliers / 100, (100 - args.outliers) / 100]
boundaries = np.nanquantile(pc1['pc1'].values.astype(float), quantile)
quantiled_bins = np.linspace(boundaries[0], boundaries[1],
args.quantile)
else:
quantile = [j / (args.quantile - 1) for j in range(0, args.quantile)]
quantiled_bins = np.nanquantile(pc1['pc1'].values.astype(float),
quantile)
pc1["quantile"] = np.searchsorted(quantiled_bins,
pc1['pc1'].values.astype(float),
side="right")
pc1.loc[pc1["pc1"] == np.nan]["quantile"] = args.quantile + 1
polarization_ratio = []
output_matrices = []
labels = []
for matrix in args.obsexp_matrices:
obs_exp = hm.hiCMatrix(matrix)
pc1["bin_id"] = pc1.apply(lambda row: get_indices(obs_exp, row),
axis=1)
name = ".".join(matrix.split("/")[-1].split(".")[0:-1])
labels.append(name)
normalised_sum_per_quantile = count_interactions(
obs_exp, pc1, args.quantile, args.offset)
normalised_sum_per_quantile = np.nan_to_num(
normalised_sum_per_quantile)
if args.outputMatrix:
output_matrices.append(normalised_sum_per_quantile)
polarization_ratio.append(
within_vs_between_compartments(normalised_sum_per_quantile,
args.quantile))
if args.outputMatrix:
np.savez(args.outputMatrix, [matrix for matrix in output_matrices])
plot_polarization_ratio(polarization_ratio, args.outputFileName, labels,
args.quantile)
def main(args=None):
args = parse_arguments().parse_args(args)
hic_matrix_list = []
sum_list = []
for matrix in args.matrices:
hic_ma = hm.hiCMatrix(matrix)
if args.normalize == 'smallest':
sum_list.append(hic_ma.matrix.sum())
hic_matrix_list.append(hic_ma)
if args.normalize == 'norm_range':
for i, hic_matrix in enumerate(hic_matrix_list):
hic_matrix.matrix.data = hic_matrix.matrix.data.astype(np.float32)
mask = np.isnan(hic_matrix.matrix.data)
hic_matrix.matrix.data[mask] = 0
mask = np.isinf(hic_matrix.matrix.data)
hic_matrix.matrix.data[mask] = 0
min_value = np.min(hic_matrix.matrix.data)
max_value = np.max(hic_matrix.matrix.data)
min_max_difference = np.float64(max_value - min_value)
hic_matrix.matrix.data -= min_value
hic_matrix.matrix.data /= min_max_difference
mask = np.isnan(hic_matrix.matrix.data)
hic_matrix.matrix.data[mask] = 0
mask = np.isinf(hic_matrix.matrix.data)
hic_matrix.matrix.data[mask] = 0
hic_matrix.matrix.eliminate_zeros()
hic_matrix.save(args.outFileName[i], pApplyCorrection=False)
elif args.normalize == 'smallest':
argmin = np.argmin(sum_list)
for i, hic_matrix in enumerate(hic_matrix_list):
hic_matrix.matrix.data = hic_matrix.matrix.data.astype(np.float32)
if i != argmin:
mask = np.isnan(hic_matrix.matrix.data)
hic_matrix.matrix.data[mask] = 0
mask = np.isinf(hic_matrix.matrix.data)
hic_matrix.matrix.data[mask] = 0
adjust_factor = sum_list[i] / sum_list[argmin]
hic_matrix.matrix.data /= adjust_factor
mask = np.isnan(hic_matrix.matrix.data)
mask = np.isnan(hic_matrix.matrix.data)
hic_matrix.matrix.data[mask] = 0
mask = np.isinf(hic_matrix.matrix.data)
hic_matrix.matrix.data[mask] = 0
hic_matrix.matrix.eliminate_zeros()
hic_matrix.save(args.outFileName[i], pApplyCorrection=False)
def main(args=None):
args = parse_arguments().parse_args(args)
hic_ma = hm.hiCMatrix(pMatrixFile=args.matrix)
indices_values = []
with open(args.regions, 'r') as file:
for line in file.readlines():
_line = line.strip().split('\t')
if len(line) == 0:
continue
if len(_line) == 2:
chrom, start = _line[0], _line[1]
viewpoint = (chrom, start, start)
elif len(_line) >= 3:
chrom, start, end = _line[0], _line[1], _line[2]
viewpoint = (chrom, start, end)
if args.range:
start_range_genomic, end_range_genomic, start_out, end_out = calculateViewpointRange(hic_ma, viewpoint, args.range, args.coordinatesToBinMapping)
start_bin, end_bin = getBinIndices(hic_ma, (chrom, start_range_genomic, end_range_genomic))
else:
start_bin, end_bin, start_out, end_out = calculateViewpointRangeBins(hic_ma, viewpoint, args.rangeInBins, args.coordinatesToBinMapping)
indices_values.append([start_bin, end_bin, start_out, end_out])
if args.range:
dimensions_new_matrix = (args.range[0] // hic_ma.getBinSize()) + (args.range[1] // hic_ma.getBinSize())
elif args.rangeInBins:
dimensions_new_matrix = args.rangeInBins[0] + args.rangeInBins[1]
summed_matrix = lil_matrix((dimensions_new_matrix, dimensions_new_matrix), dtype=np.float32)
count_matrix = np.zeros(shape=(dimensions_new_matrix, dimensions_new_matrix))
# max_length = hic_ma.matrix.shape[1]
for start, end, start_out, end_out in indices_values:
_start = 0
_end = summed_matrix.shape[1]
# if start < 0:
# _start = np.absolute(start)
# start = 0
# if end >= max_length:
# _end = end
# end = max_length
orig_matrix_length = end - start
if start_out:
_start = _end - orig_matrix_length
if end_out:
_end = start + orig_matrix_length
count_matrix[_start:_end, _start:_end] += 1
summed_matrix[_start:_end, _start:_end] += hic_ma.matrix[start:end, start:end]
summed_matrix /= count_matrix
summed_matrix = np.array(summed_matrix)
data = summed_matrix[np.nonzero(summed_matrix)]
row = np.nonzero(summed_matrix)[0]
col = np.nonzero(summed_matrix)[1]
summed_matrix = csr_matrix((data, (row, col)), shape=(dimensions_new_matrix, dimensions_new_matrix))
save_npz(args.outFileName, summed_matrix)
def test_hic_transfer_obs_exp_non_zero_perChromosome():
outfile = NamedTemporaryFile(suffix='obs_exp_.cool', delete=False)
outfile.close()
args = "--matrix {} --outFileName {} --method obs_exp_non_zero --perChromosome".format(
original_matrix_cool, outfile.name).split()
# hicTransform.main(args)
compute(hicTransform.main, args, 5)
test = hm.hiCMatrix(ROOT +
"hicTransform/obs_exp_non_zero_per_chromosome.cool")
new = hm.hiCMatrix(outfile.name)
nt.assert_array_almost_equal(test.matrix.data,
new.matrix.data,
decimal=DELTA_DECIMAL)
os.unlink(outfile.name)
def test_save():
"""
Test will not cover testing of following formats due to unsupported file_formats (see __init__ of class hiCMatrix):
* ren
* lieberman
* GInteractions
see also single test for these formats (marked as xfail)
"""
outfile_cool = NamedTemporaryFile(suffix='.cool', delete=False)
outfile_cool.close()
outfile_h5 = NamedTemporaryFile(suffix='.cool', delete=False)
outfile_h5.close()
# matrix_h5 = '/tmp/matrix.h5'
# matrix_cool = '/tmp/matrix.cool'
# matrix_npz = '/tmp/matrix.npz'
# matrix_gz = '/tmp/matrix.gz'
hic = hm.hiCMatrix()
cut_intervals = [('a', 0, 10, 1), ('a', 10, 20, 1), ('a', 20, 30, 1),
('a', 30, 40, 1), ('b', 40, 50, 1)]
hic.nan_bins = []
matrix = np.array([[1, 8, 5, 3, 0], [0, 4, 15, 5, 1], [0, 0, 0, 0, 2],
[0, 0, 0, 0, 1], [0, 0, 0, 0, 0]])
hic.matrix = csr_matrix(matrix)
hic.setMatrix(hic.matrix, cut_intervals)
hic.fillLowerTriangle()
# test .h5
hic.save(outfile_h5.name)
h5_test = hm.hiCMatrix(outfile_h5.name)
# test cool
hic.save(outfile_cool.name)
cool_test = hm.hiCMatrix(outfile_cool.name)
nt.assert_equal(hic.getMatrix(), h5_test.getMatrix())
nt.assert_equal(hic.getMatrix(), cool_test.getMatrix())
def main(args=None):
args = parse_arguments().parse_args(args)
if args.operation not in ['diff', 'ratio', 'log2ratio']:
exit("Operation not found. Please use 'diff', 'ratio' or 'log2ratio'.")
hic1 = hm.hiCMatrix(args.matrices[0])
hic2 = hm.hiCMatrix(args.matrices[1])
if hic1.matrix.shape != hic2.matrix.shape:
exit(
"The two matrices have different size. Use matrices having the same resolution and created using"
"the same parameters. Check the matrix values using the tool `hicInfo`."
)
if hic1.chrBinBoundaries != hic2.chrBinBoundaries:
exit(
"The two matrices have different chromosome order. Use the tool `hicExport` to change the order.\n"
"{}: {}\n"
"{}: {}".format(args.matrices[0], hic1.chrBinBoundaries.keys(),
args.matrices[1], hic2.chrBinBoundaries.keys()))
# normalize by total matrix sum
hic1.matrix.data = hic1.matrix.data.astype(float) / hic1.matrix.data.sum()
hic2.matrix.data = hic2.matrix.data.astype(float) / hic2.matrix.data.sum()
nan_bins = set(hic1.nan_bins)
nan_bins = nan_bins.union(hic2.nan_bins)
if args.operation == 'diff':
new_matrix = hic1.matrix - hic2.matrix
elif args.operation == 'ratio' or args.operation == 'log2ratio':
hic2.matrix.data = float(1) / hic2.matrix.data
new_matrix = hic1.matrix.multiply(hic2.matrix)
# just in case
new_matrix.eliminate_zeros()
if args.operation == 'log2ratio':
new_matrix.data = np.log2(new_matrix.data)
new_matrix.eliminate_zeros()
hic1.setMatrixValues(new_matrix)
hic1.maskBins(sorted(nan_bins))
hic1.save(args.outFileName)
def test_plot_chromosomes():
outfile_density = NamedTemporaryFile(suffix='.png', delete=False)
outfile_density.close()
outfile_coverage = NamedTemporaryFile(suffix='.png', delete=False)
outfile_coverage.close()
outfile_qc_report = NamedTemporaryFile(suffix='.txt', delete=False)
outfile_qc_report.close()
outfile_matrix = NamedTemporaryFile(suffix='.mcool', delete=False)
outfile_matrix.close()
args = "--matrix {} --outputMcool {} -t {} --dpi {} --outFileNameDensity {} \
--outFileNameReadCoverage {} --outFileNameQCReport {} \
--minimumReadCoverage {} --minimumDensity {} \
--maximumRegionToConsider {} --chromosomes chr1 chr2".format(ROOT + 'test_matrix.mcool',
outfile_matrix.name, 1, 300,
outfile_density.name,
outfile_coverage.name,
outfile_qc_report.name,
100000, 0.001, 30000000
).split()
scHicQualityControl.main(args)
test_image_density = ROOT + 'scHicQualityControl/density_chr1_chr2.png'
res = compare_images(test_image_density, outfile_density.name, tolerance)
assert res is None, res
test_image_density = ROOT + 'scHicQualityControl/coverage_chr1_chr2.png'
res = compare_images(test_image_density, outfile_coverage.name, tolerance)
assert res is None, res
assert are_files_equal(ROOT + "scHicQualityControl/qc_report_chr1_chr2.txt", outfile_qc_report.name)
test_data_matrix = ROOT + 'scHicQualityControl/qc_matrix_chr1_chr2.mcool'
matrices_list_test_data = cooler.fileops.list_coolers(test_data_matrix)
matrices_list_created = cooler.fileops.list_coolers(outfile_matrix.name)
matrices_list_test_data = sorted(matrices_list_test_data)
matrices_list_created = sorted(matrices_list_created)
for test_matrix, created_matrix in zip(matrices_list_test_data, matrices_list_created):
test = hm.hiCMatrix(test_data_matrix + '::' + test_matrix)
created = hm.hiCMatrix(outfile_matrix.name + '::' + created_matrix)
nt.assert_almost_equal(test.matrix.data, created.matrix.data, decimal=5)
nt.assert_equal(test.cut_intervals, created.cut_intervals)
def create_bulk_matrix(pMatrixName, pMatricesList, pQueue):
bulk_matrix = None
for i, matrix in enumerate(pMatricesList):
hic_matrix_obj = hm.hiCMatrix(pMatrixFile=pMatrixName + '::' + matrix)
if bulk_matrix is None:
bulk_matrix = hic_matrix_obj
else:
bulk_matrix.matrix += hic_matrix_obj.matrix
pQueue.put(bulk_matrix)
return
def run_target_list_compilation(pInteractionFilesList,
pTargetList,
pArgs,
pViewpointObj,
pQueue=None,
pOneTarget=False):
outfile_names_list = []
accepted_scores_list = []
target_regions_intervaltree = None
try:
if pOneTarget == True:
try:
target_regions = utilities.readBed(pTargetList)
except Exception as exp:
pQueue.put('Fail: ' + str(exp) + traceback.format_exc())
return
hicmatrix = hm.hiCMatrix()
target_regions_intervaltree = hicmatrix.intervalListToIntervalTree(
target_regions)[0]
for i, interactionFile in enumerate(pInteractionFilesList):
outfile_names_list_intern = []
accepted_scores_list_intern = []
for sample in interactionFile:
interaction_data, interaction_file_data, _ = pViewpointObj.readInteractionFile(
pArgs.interactionFile, sample)
if pOneTarget == True:
target_file = None
else:
target_file = pTargetList[i]
accepted_scores = filter_scores_target_list(
interaction_file_data,
pTargetList=target_file,
pTargetIntervalTree=target_regions_intervaltree,
pTargetFile=pArgs.targetFile)
outfile_names_list_intern.append(sample)
accepted_scores_list_intern.append(accepted_scores)
outfile_names_list.append(outfile_names_list_intern)
accepted_scores_list.append(accepted_scores_list_intern)
except Exception as exp:
pQueue.put('Fail: ' + str(exp) + traceback.format_exc())
return
if pQueue is None:
return
counter = 0
for item in accepted_scores_list_intern:
if len(item) == 0:
counter += 1
pQueue.put([outfile_names_list, accepted_scores_list])
return
def filter_scores_target_list(pScoresDictionary,
pTargetList=None,
pTargetIntervalTree=None):
accepted_scores = {}
same_target_dict = {}
target_regions_intervaltree = None
if pTargetList is not None:
target_regions = utilities.readBed(pTargetList)
if len(target_regions) == 0:
return accepted_scores
hicmatrix = hm.hiCMatrix()
target_regions_intervaltree = hicmatrix.intervalListToIntervalTree(
target_regions)[0]
elif pTargetIntervalTree is not None:
target_regions_intervaltree = pTargetIntervalTree
else:
log.error('No target list given.')
exit(1)
for key in pScoresDictionary:
# try:
chromosome = pScoresDictionary[key][0]
start = int(pScoresDictionary[key][1])
end = int(pScoresDictionary[key][2])
if chromosome in target_regions_intervaltree:
target_interval = target_regions_intervaltree[chromosome][
start:end]
else:
continue
if target_interval:
target_interval = sorted(target_interval)[0]
if target_interval in same_target_dict:
same_target_dict[target_interval].append(key)
else:
same_target_dict[target_interval] = [key]
for target in same_target_dict:
values = np.array([0.0, 0.0, 0.0])
same_target_dict[target] = sorted(same_target_dict[target])
for key in same_target_dict[target]:
values += np.array(list(map(float, pScoresDictionary[key][-3:])))
new_data_line = pScoresDictionary[same_target_dict[target][0]]
new_data_line[2] = pScoresDictionary[same_target_dict[target][-1]][2]
new_data_line[-5] = pScoresDictionary[same_target_dict[target][-1]][-5]
new_data_line[-3] = values[0]
new_data_line[-2] = values[1]
new_data_line[-1] = values[2]
accepted_scores[same_target_dict[target][0]] = new_data_line
return accepted_scores
def main(args=None):
args = parse_arguments().parse_args(args)
hic = hm.hiCMatrix(args.matrix)
if args.runningWindow:
merged_matrix = running_window_merge(hic, args.numBins)
else:
merged_matrix = merge_bins(hic, args.numBins)
merged_matrix.save(args.outFileName)
def test_build_matrix_cooler_metadata():
outfile = NamedTemporaryFile(suffix='.cool', delete=False)
outfile.close()
outfile_bam = NamedTemporaryFile(suffix='.bam', delete=False)
outfile.close()
qc_folder = mkdtemp(prefix="testQC_")
args = "-s {} {} --outFileName {} -bs 5000 -b {} --QCfolder {} --threads 4 --genomeAssembly dm3 \
--restrictionSequence GATC --danglingSequence GATC -rs {}".format(
sam_R1, sam_R2, outfile.name, outfile_bam.name, qc_folder,
dpnii_file).split()
# hicBuildMatrix.main(args)
compute(hicBuildMatrix.main, args, 5)
test = hm.hiCMatrix(ROOT + "small_test_matrix_parallel.h5")
new = hm.hiCMatrix(outfile.name)
nt.assert_equal(test.matrix.data, new.matrix.data)
# nt.assert_equal(test.cut_intervals, new.cut_intervals)
nt.assert_equal(len(new.cut_intervals), len(test.cut_intervals))
cut_interval_new_ = []
cut_interval_test_ = []
for x in new.cut_intervals:
cut_interval_new_.append(x[:3])
for x in test.cut_intervals:
cut_interval_test_.append(x[:3])
nt.assert_equal(cut_interval_new_, cut_interval_test_)
# print(set(os.listdir(ROOT + "QC/")))
assert are_files_equal(ROOT + "QC/QC.log", qc_folder + "/QC.log")
assert set(os.listdir(ROOT + "QC/")) == set(os.listdir(qc_folder))
outfile_metadata = NamedTemporaryFile(suffix='.txt', delete=False)
outfile_metadata.close()
args = "-m {} -o {}".format(outfile.name, outfile_metadata.name).split()
hicInfo.main(args)
assert are_files_equal(ROOT + "hicBuildMatrix/metadata.txt",
outfile_metadata.name,
delta=7)
os.unlink(outfile.name)
shutil.rmtree(qc_folder)
def test_normalize_smallest_h5_cool_equal(capsys):
outfile_one = NamedTemporaryFile(suffix='.cool', delete=False)
outfile_one.close()
outfile_one_cool = NamedTemporaryFile(suffix='.cool', delete=False)
outfile_one.close()
outfile_two = NamedTemporaryFile(suffix='.h5', delete=False)
outfile_two.close()
outfile_two_h5 = NamedTemporaryFile(suffix='.h5', delete=False)
outfile_two.close()
args = "--matrices {} {} --normalize smallest -o {} {}".format(
matrix_one_cool, matrix_two_cool, outfile_one.name,
outfile_one_cool.name).split()
# hicNormalize.main(args)
compute(hicNormalize.main, args, 5)
args = "--matrices {} {} --normalize smallest -o {} {}".format(
matrix_one_h5, matrix_two_h5, outfile_two.name,
outfile_two_h5.name).split()
# hicNormalize.main(args)
compute(hicNormalize.main, args, 5)
test_one = hm.hiCMatrix(ROOT + "/smallest_one.cool")
test_two = hm.hiCMatrix(ROOT + "/smallest_one.h5")
new_one = hm.hiCMatrix(outfile_one_cool.name)
new_two = hm.hiCMatrix(outfile_two_h5.name)
nt.assert_equal(test_one.matrix.data, new_one.matrix.data)
nt.assert_equal(test_one.cut_intervals, new_one.cut_intervals)
nt.assert_equal(test_two.matrix.data, new_two.matrix.data)
nt.assert_equal(test_two.cut_intervals, new_two.cut_intervals)
nt.assert_equal(new_one.matrix.data, new_two.matrix.data)
nt.assert_equal(len(new_one.cut_intervals), len(new_two.cut_intervals))
os.unlink(outfile_one.name)
os.unlink(outfile_two.name)
def main(args=None):
args = parse_arguments().parse_args(args)
hic_ma = hm.hiCMatrix(args.matrix)
hic_ma.restoreMaskedBins()
# the bin id of boundary positions
boundary_id_list = get_boundary_bin_id(hic_ma, args.domains)
# make a reduce matrix by merging the TAD bins
log.info("Generating matrix with merged bins")
merge_tad_bins(hic_ma, boundary_id_list, args.outFile)
def test_hic_transfer_all():
outfile = NamedTemporaryFile(suffix='all.h5', delete=False)
outfile.close()
args = "--matrix {} --outFileName {} --method all".format(
original_matrix, outfile.name).split()
hicTransform.main(args)
dirname_new = dirname(outfile.name)
basename_new = basename(outfile.name)
# obs_exp
test = hm.hiCMatrix(ROOT + "hicTransform/obs_exp_small_50kb.h5")
new = hm.hiCMatrix(dirname_new + "/obs_exp_" + basename_new)
nt.assert_array_almost_equal(test.matrix.data,
new.matrix.data,
decimal=DELTA_DECIMAL)
os.unlink(dirname_new + "/obs_exp_" + basename_new)
# pearson
test = hm.hiCMatrix(ROOT + "hicTransform/pearson_small_50kb.h5")
new = hm.hiCMatrix(dirname_new + "/pearson_" + basename_new)
nt.assert_array_almost_equal(test.matrix.data,
new.matrix.data,
decimal=DELTA_DECIMAL)
os.unlink(dirname_new + "/pearson_" + basename_new)
# covariance
test = hm.hiCMatrix(ROOT + "hicTransform/covariance_small_50kb.h5")
new = hm.hiCMatrix(dirname_new + "/covariance_" + basename_new)
nt.assert_array_almost_equal(test.matrix.data,
new.matrix.data,
decimal=DELTA_DECIMAL)
os.unlink(dirname_new + "/covariance_" + basename_new)
os.unlink(outfile.name)
def test_filterOutInterChrCounts():
hic = hm.hiCMatrix()
cut_intervals = [('a', 0, 10, 1), ('a', 10, 20, 1), ('a', 20, 30, 1),
('b', 30, 40, 1), ('b', 40, 50, 1)]
hic.nan_bins = []
matrix = np.array([[1, 8, 5, 3, 0], [0, 4, 15, 5, 1], [0, 0, 0, 0, 2],
[0, 0, 0, 0, 1], [0, 0, 0, 0, 0]])
hic.matrix = csr_matrix(matrix)
hic.setMatrix(hic.matrix, cut_intervals)
hic.fillLowerTriangle()
hic.filterOutInterChrCounts()
filtered_matrix = np.matrix([[1, 8, 5, 0, 0], [8, 4, 15, 0, 0],
[5, 15, 0, 0, 0], [0, 0, 0, 0, 1],
[0, 0, 0, 1, 0]])
nt.assert_equal(hic.getMatrix(), filtered_matrix)
row, col = np.triu_indices(5)
cut_intervals = [('a', 0, 10, 1), ('a', 10, 20, 1), ('a', 20, 30, 1),
('b', 30, 40, 1), ('b', 40, 50, 1)]
hic = hm.hiCMatrix()
hic.nan_bins = []
matrix = np.array([[0, 10, 5, 3, 0], [0, 0, 15, 5, 1], [0, 0, 0, 7, 3],
[0, 0, 0, 0, 1], [0, 0, 0, 0, 0]])
# make the matrix symmetric:
hic.matrix = csr_matrix(matrix + matrix.T)
hic.setMatrix(csr_matrix(matrix + matrix.T, dtype=np.int32), cut_intervals)
filtered = hic.filterOutInterChrCounts().todense()
test_matrix = np.array(
[[0, 10, 5, 0, 0], [10, 0, 15, 0, 0], [5, 15, 0, 0, 0],
[0, 0, 0, 0, 1], [0, 0, 0, 1, 0]],
dtype='i4')
nt.assert_equal(filtered, test_matrix)
def test_convert_to_zscore_matrix_2():
# load test matrix
hic = hm.hiCMatrix(ROOT + 'Li_et_al_2015.h5')
hic.maskBins(hic.nan_bins)
mat = hic.matrix.todense()
max_depth = 10000
bin_size = hic.getBinSize()
max_depth_in_bins = int(float(max_depth) / bin_size)
m_size = mat.shape[0]
# compute matrix values per distance
chrom, start, end, extra = zip(
*hm.hiCMatrix.fit_cut_intervals(hic.cut_intervals))
dist_values = {}
sys.stderr.write("Computing values per distance for each matrix entry\n")
for _i in range(mat.shape[0]):
for _j in range(mat.shape[0]):
if _j >= _i:
# dist is translated to bins
dist = int(float(start[_j] - start[_i]) / bin_size)
if dist <= max_depth_in_bins:
if dist not in dist_values:
dist_values[dist] = []
dist_values[dist].append(mat[_i, _j])
mu = {}
std = {}
for dist, values in iteritems(dist_values):
mu[dist] = np.mean(values)
std[dist] = np.std(values)
# compute z-score for test matrix
sys.stderr.write("Computing zscore for each matrix entry\n")
zscore_mat = np.full((m_size, m_size), np.nan)
for _i in range(mat.shape[0]):
for _j in range(mat.shape[0]):
if _j >= _i:
dist = int(float(start[_j] - start[_i]) / bin_size)
if dist <= max_depth_in_bins:
zscore = (mat[_i, _j] - mu[dist]) / std[dist]
zscore_mat[_i, _j] = zscore
# compare with zscore from class
hic.convert_to_zscore_matrix(maxdepth=max_depth)
# from numpy.testing import assert_almost_equal
# only the main diagonal is check. Other diagonals show minimal differences
nt.assert_almost_equal(hic.matrix.todense().diagonal(0).A1,
zscore_mat.diagonal(0))
def test_intervalListToIntervalTree(capsys):
# get matrix
hic = hm.hiCMatrix()
cut_intervals = [('a', 0, 10, 1), ('a', 10, 20, 1), ('a', 20, 30, 1),
('b', 30, 40, 1), ('b', 40, 50, 1)]
hic.nan_bins = []
matrix = np.array([[1, 8, 5, 3, 0], [0, 4, 15, 5, 1], [0, 0, 0, 0, 2],
[0, 0, 0, 0, 1], [0, 0, 0, 0, 0]])
hic.matrix = csr_matrix(matrix)
hic.setMatrix(hic.matrix, cut_intervals)
nt.assert_equal(hic.getMatrix(), matrix)
# empty list should raise AssertionError
interval_list = []
with pytest.raises(AssertionError):
hic.intervalListToIntervalTree(interval_list)
captured = capsys.readouterr()
assert captured.out == "Interval list is empty"
# test with correct interval_list
interval_list = [('a', 0, 10, 1), ('a', 10, 20, 1), ('b', 20, 30, 1),
('b', 30, 50, 1), ('b', 50, 100, 1), ('c', 100, 200, 1),
('c', 200, 210, 1), ('d', 210, 220, 1), ('e', 220, 250)]
tree, boundaries = hic.intervalListToIntervalTree(interval_list)
# test tree
nt.assert_equal(tree['a'],
IntervalTree([Interval(0, 10, 0),
Interval(10, 20, 1)]))
nt.assert_equal(
tree['b'],
IntervalTree(
[Interval(20, 30, 2),
Interval(30, 50, 3),
Interval(50, 100, 4)]))
nt.assert_equal(
tree['c'], IntervalTree([Interval(100, 200, 5),
Interval(200, 210, 6)]))
nt.assert_equal(tree['d'], IntervalTree([Interval(210, 220, 7)]))
nt.assert_equal(tree['e'], IntervalTree([Interval(220, 250, 8)]))
# test boundaries
nt.assert_equal(
boundaries,
OrderedDict([('a', (0, 2)), ('b', (2, 5)), ('c', (5, 7)),
('d', (7, 8)), ('e', (8, 9))]))
def test_merge_matrices_running_window():
outfile = NamedTemporaryFile(suffix='.mcool', delete=False)
outfile.close()
args = "--matrix {} --outFileName {} -t {} -nb {} --runningWindow".format(ROOT + 'test_matrix.mcool',
outfile.name, 1, 11).split()
scHicMergeMatrixBins.main(args)
test_data_matrix = ROOT + 'scHicMergeMatrixBins/test_matrix_10mb_running_window.mcool'
matrices_list_test_data = cooler.fileops.list_coolers(test_data_matrix)
matrices_list_created = cooler.fileops.list_coolers(outfile.name)
matrices_list_test_data = sorted(matrices_list_test_data)
matrices_list_created = sorted(matrices_list_created)
for test_matrix, created_matrix in zip(matrices_list_test_data, matrices_list_created):
test = hm.hiCMatrix(test_data_matrix + '::' + test_matrix)
created = hm.hiCMatrix(outfile.name + '::' + created_matrix)
nt.assert_almost_equal(test.matrix.data, created.matrix.data, decimal=5)
nt.assert_equal(test.cut_intervals, created.cut_intervals)
os.unlink(outfile.name)
def compute_contains_all_chromosomes(pMatrixName, pMatricesList, pChromosomes, pQueue):
keep_matrices_chromosome_names = []
for i, matrix in enumerate(pMatricesList):
ma = hm.hiCMatrix(pMatrixName + '::' + matrix)
if pChromosomes is None:
pChromosomes = list(ma.chrBinBoundaries)
try:
ma.keepOnlyTheseChr(pChromosomes)
keep_matrices_chromosome_names.append(1)
except Exception:
keep_matrices_chromosome_names.append(0)
pQueue.put(keep_matrices_chromosome_names)
def test_find_TADs_fdr_chromosomes():
# full test case with build of the matrix and search for tads
matrix = ROOT + "small_test_matrix.h5"
tad_folder = mkdtemp(prefix="test_case_find_tads_fdr_chromosomes")
args = "--matrix {} --minDepth 60000 --maxDepth 180000 --numberOfProcessors 2 --step 20000 \
--outPrefix {}/test_multiFDR_chromosomes --minBoundaryDistance 20000 \
--correctForMultipleTesting fdr --thresholdComparisons 0.5 --chromosomes chr2L chr3R".format(
matrix, tad_folder).split()
# hicFindTADs.main(args)
compute(hicFindTADs.main, args, 5)
new = hm.hiCMatrix(tad_folder +
"/test_multiFDR_chromosomes_zscore_matrix.h5")
test = hm.hiCMatrix(ROOT +
'find_TADs/FDR_chromosomes/multiFDR_zscore_matrix.h5')
nt.assert_equal(test.matrix.data, new.matrix.data)
nt.assert_equal(test.cut_intervals, new.cut_intervals)
print(tad_folder + "/test_multiFDR_boundaries.bed")
assert are_files_equal(
ROOT + "find_TADs/FDR_chromosomes/multiFDR_boundaries.bed",
tad_folder + "/test_multiFDR_chromosomes_boundaries.bed")
assert are_files_equal(
ROOT + "find_TADs/FDR_chromosomes/multiFDR_domains.bed",
tad_folder + "/test_multiFDR_chromosomes_domains.bed")
assert are_files_equal(
ROOT + "find_TADs/FDR_chromosomes/multiFDR_tad_score.bm",
tad_folder + "/test_multiFDR_chromosomes_tad_score.bm")
assert are_files_equal(
ROOT + "find_TADs/FDR_chromosomes/multiFDR_boundaries.gff",
tad_folder + "/test_multiFDR_chromosomes_boundaries.gff")
# assert are_files_equal
assert are_files_equal(
ROOT + "find_TADs/FDR_chromosomes/multiFDR_score.bedgraph",
tad_folder + "/test_multiFDR_chromosomes_score.bedgraph")
shutil.rmtree(tad_folder)
def test_build_matrix_cooler_multiple():
outfile = NamedTemporaryFile(suffix='.cool', delete=False)
outfile.close()
qc_folder = mkdtemp(prefix="testQC_")
args = "-s {} {} --outFileName {} -bs 5000 10000 20000 -b /tmp/test.bam --QCfolder {} --threads 4".format(sam_R1, sam_R2,
outfile.name,
qc_folder).split()
hicBuildMatrix.main(args)
test_5000 = hm.hiCMatrix(ROOT + "hicBuildMatrix/multi_small_test_matrix.cool::/resolutions/5000")
test_10000 = hm.hiCMatrix(ROOT + "hicBuildMatrix/multi_small_test_matrix.cool::/resolutions/10000")
test_20000 = hm.hiCMatrix(ROOT + "hicBuildMatrix/multi_small_test_matrix.cool::/resolutions/20000")
new_5000 = hm.hiCMatrix(outfile.name + '::/resolutions/5000')
new_10000 = hm.hiCMatrix(outfile.name + '::/resolutions/10000')
new_20000 = hm.hiCMatrix(outfile.name + '::/resolutions/20000')
nt.assert_equal(test_5000.matrix.data, new_5000.matrix.data)
nt.assert_equal(test_10000.matrix.data, new_10000.matrix.data)
nt.assert_equal(test_20000.matrix.data, new_20000.matrix.data)
# nt.assert_equal(test.cut_intervals, new.cut_intervals)
nt.assert_equal(len(new_5000.cut_intervals), len(test_5000.cut_intervals))
nt.assert_equal(len(new_10000.cut_intervals), len(test_10000.cut_intervals))
nt.assert_equal(len(new_20000.cut_intervals), len(test_20000.cut_intervals))
cut_interval_new_ = []
cut_interval_test_ = []
for x in new_5000.cut_intervals:
cut_interval_new_.append(x[:3])
for x in test_5000.cut_intervals:
cut_interval_test_.append(x[:3])
nt.assert_equal(cut_interval_new_, cut_interval_test_)
cut_interval_new_ = []
cut_interval_test_ = []
for x in new_10000.cut_intervals:
cut_interval_new_.append(x[:3])
for x in test_10000.cut_intervals:
cut_interval_test_.append(x[:3])
nt.assert_equal(cut_interval_new_, cut_interval_test_)
cut_interval_new_ = []
cut_interval_test_ = []
for x in new_20000.cut_intervals:
cut_interval_new_.append(x[:3])
for x in test_20000.cut_intervals:
cut_interval_test_.append(x[:3])
nt.assert_equal(cut_interval_new_, cut_interval_test_)
# print(set(os.listdir(ROOT + "QC/")))
assert are_files_equal(ROOT + "QC/QC.log", qc_folder + "/QC.log")
assert set(os.listdir(ROOT + "QC/")) == set(os.listdir(qc_folder))
os.unlink(outfile.name)
shutil.rmtree(qc_folder)
def open_and_store_matrix(pMatrixName, pMatricesList, pIndex, pXDimension, pChromosomes, pQueue):
neighborhood_matrix = None
for i, matrix in enumerate(pMatricesList):
if pChromosomes is not None and len(pChromosomes) == 1:
hic_ma = hm.hiCMatrix(pMatrixFile=pMatrixName + '::' + matrix, pChrnameList=pChromosomes)
else:
hic_ma = hm.hiCMatrix(pMatrixFile=pMatrixName + '::' + matrix)
if pChromosomes:
hic_ma.keepOnlyTheseChr(pChromosomes)
_matrix = hic_ma.matrix
if neighborhood_matrix is None:
neighborhood_matrix = csr_matrix((pXDimension, _matrix.shape[0] * _matrix.shape[1]), dtype=np.float)
instances, features = _matrix.nonzero()
instances *= _matrix.shape[1]
instances += features
features = None
neighborhood_matrix[pIndex + i, instances] = _matrix.data
pQueue.put(neighborhood_matrix)
def run_target_list_compilation(pInteractionFilesList, pTargetList, pArgs, pViewpointObj, pQueue=None):
outfile_names = []
target_regions_intervaltree = None
if pArgs.batchMode and len(pTargetList) == 1:
target_regions = utilities.readBed(pTargetList[0])
hicmatrix = hm.hiCMatrix()
target_regions_intervaltree = hicmatrix.intervalListToIntervalTree(target_regions)[0]
for i, interactionFile in enumerate(pInteractionFilesList):
for sample in interactionFile:
if pArgs.interactionFileFolder != '.':
absolute_sample_path = pArgs.interactionFileFolder + '/' + sample
else:
absolute_sample_path = sample
header, interaction_data, interaction_file_data = pViewpointObj.readInteractionFileForAggregateStatistics(
absolute_sample_path)
log.debug('len(pTargetList) {}'.format(len(pTargetList)))
if pArgs.batchMode and len(pTargetList) > 1:
if pArgs.targetFileFolder != '.':
target_file = pArgs.targetFileFolder + '/' + pTargetList[i]
else:
target_file = pTargetList[i]
elif pArgs.batchMode and len(pTargetList) == 1:
target_file = None
else:
target_file = pTargetList[i]
accepted_scores = filter_scores_target_list(interaction_file_data, pTargetList=target_file, pTargetIntervalTree=target_regions_intervaltree)
if len(accepted_scores) == 0:
# do not call 'break' or 'continue'
# with this an empty file is written and no track of 'no significant interactions' detected files needs to be recorded.
if pArgs.batchMode:
with open('errorLog.txt', 'a+') as errorlog:
errorlog.write('Failed for: {} and {}.\n'.format(interactionFile[0], interactionFile[1]))
else:
log.info('No target regions found')
outFileName = '.'.join(sample.split('/')[-1].split('.')[:-1]) + '_' + pArgs.outFileNameSuffix
if pArgs.batchMode:
outfile_names.append(outFileName)
if pArgs.outputFolder != '.':
outFileName = pArgs.outputFolder + '/' + outFileName
write(outFileName, header, accepted_scores,
interaction_file_data)
if pQueue is None:
return
pQueue.put(outfile_names)
return
def test_maskChromosomes():
hic = hm.hiCMatrix()
cut_intervals = [('a', 0, 10, 1), ('a', 10, 20, 1), ('a', 20, 30, 1),
('b', 30, 40, 1), ('b', 40, 50, 1)]
hic.nan_bins = []
matrix = np.array([[1, 8, 5, 3, 0], [0, 4, 15, 5, 1], [0, 0, 0, 0, 2],
[0, 0, 0, 0, 1], [0, 0, 0, 0, 0]])
hic.matrix = csr_matrix(matrix)
hic.setMatrix(hic.matrix, cut_intervals)
hic.maskChromosomes(['a'])