def _obs_exp_lieberman(pSubmatrix, pLengthChromosome, pChromosomeCount):
obs_exp_matrix_ = obs_exp_matrix_lieberman(pSubmatrix, pLengthChromosome,
pChromosomeCount)
obs_exp_matrix_ = convertNansToZeros(csr_matrix(obs_exp_matrix_))
obs_exp_matrix_ = convertInfsToZeros(csr_matrix(obs_exp_matrix_)).todense()
return obs_exp_matrix_
def _pearson(pSubmatrix):
pearson_correlation_matrix = np.corrcoef(pSubmatrix)
pearson_correlation_matrix = convertNansToZeros(
csr_matrix(pearson_correlation_matrix))
pearson_correlation_matrix = convertInfsToZeros(
csr_matrix(pearson_correlation_matrix)).todense()
return pearson_correlation_matrix
def _pearson(pSubmatrix):
pearson_correlation_matrix = np.corrcoef(pSubmatrix)
pearson_correlation_matrix = convertNansToZeros(csr_matrix(pearson_correlation_matrix))
pearson_correlation_matrix = convertInfsToZeros(csr_matrix(pearson_correlation_matrix))
# if len(pearson_correlation_matrix.data) == 0:
# return np.array([[]])
return pearson_correlation_matrix # .todense()
def __obs_exp(pSubmatrix, pLengthChromosome, pChromosomeCount):
exp_obs_matrix_ = exp_obs_matrix_lieberman(pSubmatrix, pLengthChromosome,
pChromosomeCount)
exp_obs_matrix_ = convertNansToZeros(csr_matrix(exp_obs_matrix_))
exp_obs_matrix_ = convertInfsToZeros(csr_matrix(exp_obs_matrix_)).todense()
return exp_obs_matrix_
def _obs_exp_non_zero(pSubmatrix, ligation_factor):
obs_exp_matrix_ = obs_exp_matrix_non_zero(pSubmatrix, ligation_factor)
obs_exp_matrix_ = convertNansToZeros(csr_matrix(obs_exp_matrix_))
obs_exp_matrix_ = convertInfsToZeros(csr_matrix(obs_exp_matrix_))
# if len(obs_exp_matrix_.data) == 0:
# return np.array([[]])
return obs_exp_matrix_ # .todense()
def _obs_exp(pSubmatrix):
obs_exp_matrix_ = obs_exp_matrix(pSubmatrix)
obs_exp_matrix_ = convertNansToZeros(csr_matrix(obs_exp_matrix_))
obs_exp_matrix_ = convertInfsToZeros(csr_matrix(obs_exp_matrix_))
# if len(obs_exp_matrix_.data) == 0:
# return np.array([[]])
return obs_exp_matrix_ # .todense()
def _obs_exp_lieberman(pSubmatrix, pLengthChromosome, pChromosomeCount):
obs_exp_matrix_ = obs_exp_matrix_lieberman(pSubmatrix, pLengthChromosome, pChromosomeCount)
obs_exp_matrix_ = convertNansToZeros(csr_matrix(obs_exp_matrix_))
obs_exp_matrix_ = convertInfsToZeros(csr_matrix(obs_exp_matrix_))
# if len(obs_exp_matrix_.data) == 0:
# return np.array()
return obs_exp_matrix_ # .todense()
def get_expected_matrix(pSubmatrix):
expected_interactions_in_distance = expected_interactions(pSubmatrix)
row, col = pSubmatrix.nonzero()
distance = np.ceil(np.absolute(row - col) / 2).astype(np.int32)
expected = expected_interactions_in_distance[distance]
pSubmatrix.data = expected
pSubmatrix = convertNansToZeros(csr_matrix(pSubmatrix))
pSubmatrix = convertInfsToZeros(csr_matrix(pSubmatrix)).todense()
return pSubmatrix
def _obs_exp(pSubmatrix):
obs_exp_matrix_ = obs_exp_matrix(pSubmatrix)
obs_exp_matrix_ = convertNansToZeros(csr_matrix(obs_exp_matrix_))
obs_exp_matrix_ = convertInfsToZeros(csr_matrix(obs_exp_matrix_))
# log.error('obs_exp_matrix_.data {}'.format(obs_exp_matrix_.data))
# if len(obs_exp_matrix_.data) == 0:
# log.debug('No data!')
# return np.array([[]])
return obs_exp_matrix_ # .todense()
def main(args=None):
args = parse_arguments().parse_args(args)
if int(args.numberOfEigenvectors) != len(args.outputFileName):
log.error(
"Number of output file names and number of eigenvectors does not match. Please"
"provide the name of each file.\nFiles: {}\nNumber of eigenvectors: {}"
.format(args.outputFileName, args.numberOfEigenvectors))
exit(1)
ma = hm.hiCMatrix(args.matrix)
ma.maskBins(ma.nan_bins)
if args.chromosomes:
ma.keepOnlyTheseChr(args.chromosomes)
vecs_list = []
chrom_list = []
start_list = []
end_list = []
# PCA is computed per chromosome
length_chromosome = 0
chromosome_count = len(ma.getChrNames())
if args.pearsonMatrix:
trasf_matrix_pearson = lil_matrix(ma.matrix.shape)
if args.obsexpMatrix:
trasf_matrix_obsexp = lil_matrix(ma.matrix.shape)
for chrname in ma.getChrNames():
chr_range = ma.getChrBinRange(chrname)
length_chromosome += chr_range[1] - chr_range[0]
for chrname in ma.getChrNames():
chr_range = ma.getChrBinRange(chrname)
submatrix = ma.matrix[chr_range[0]:chr_range[1],
chr_range[0]:chr_range[1]]
if args.norm:
exp_obs_matrix_ = exp_obs_matrix_norm(submatrix, length_chromosome,
chromosome_count)
exp_obs_matrix_ = convertNansToZeros(
csr_matrix(exp_obs_matrix_)).todense()
exp_obs_matrix_ = convertInfsToZeros(
csr_matrix(exp_obs_matrix_)).todense()
else:
exp_obs_matrix_ = exp_obs_matrix_lieberman(submatrix,
length_chromosome,
chromosome_count)
exp_obs_matrix_ = convertNansToZeros(
csr_matrix(exp_obs_matrix_)).todense()
exp_obs_matrix_ = convertInfsToZeros(
csr_matrix(exp_obs_matrix_)).todense()
if args.obsexpMatrix:
trasf_matrix_obsexp[chr_range[0]:chr_range[1],
chr_range[0]:chr_range[1]] = lil_matrix(
exp_obs_matrix_)
pearson_correlation_matrix = np.corrcoef(exp_obs_matrix_)
pearson_correlation_matrix = convertNansToZeros(
csr_matrix(pearson_correlation_matrix)).todense()
pearson_correlation_matrix = convertInfsToZeros(
csr_matrix(pearson_correlation_matrix)).todense()
if args.pearsonMatrix:
trasf_matrix_pearson[chr_range[0]:chr_range[1],
chr_range[0]:chr_range[1]] = lil_matrix(
pearson_correlation_matrix)
corrmatrix = np.cov(pearson_correlation_matrix)
corrmatrix = convertNansToZeros(csr_matrix(corrmatrix)).todense()
corrmatrix = convertInfsToZeros(csr_matrix(corrmatrix)).todense()
evals, eigs = linalg.eig(corrmatrix)
k = args.numberOfEigenvectors
chrom, start, end, _ = zip(
*ma.cut_intervals[chr_range[0]:chr_range[1]])
vecs_list += eigs[:, :k].tolist()
chrom_list += chrom
start_list += start
end_list += end
if args.pearsonMatrix:
file_type = 'cool'
if args.pearsonMatrix.endswith('.h5'):
file_type = 'h5'
matrixFileHandlerOutput = MatrixFileHandler(pFileType=file_type)
matrixFileHandlerOutput.set_matrix_variables(
trasf_matrix_pearson.tocsr(), ma.cut_intervals, ma.nan_bins,
ma.correction_factors, ma.distance_counts)
matrixFileHandlerOutput.save(args.pearsonMatrix,
pSymmetric=True,
pApplyCorrection=False)
if args.obsexpMatrix:
file_type = 'cool'
if args.obsexpMatrix.endswith('.h5'):
file_type = 'h5'
matrixFileHandlerOutput = MatrixFileHandler(pFileType=file_type)
matrixFileHandlerOutput.set_matrix_variables(
trasf_matrix_obsexp.tocsr(), ma.cut_intervals, ma.nan_bins,
ma.correction_factors, ma.distance_counts)
matrixFileHandlerOutput.save(args.obsexpMatrix,
pSymmetric=True,
pApplyCorrection=False)
if args.geneTrack:
vecs_list = correlateEigenvectorWithGeneTrack(ma, vecs_list,
args.geneTrack)
if args.format == 'bedgraph':
for idx, outfile in enumerate(args.outputFileName):
assert (len(vecs_list) == len(chrom_list))
with open(outfile, 'w') as fh:
for i, value in enumerate(vecs_list):
if len(value) == args.numberOfEigenvectors:
if isinstance(value[idx], np.complex):
value[idx] = value[idx].real
fh.write("{}\t{}\t{}\t{:.12f}\n".format(
toString(chrom_list[i]), start_list[i],
end_list[i], value[idx]))
elif args.format == 'bigwig':
if not pyBigWig.numpy == 1:
log.error(
"ERROR: Your version of pyBigWig is not supporting numpy: {}".
format(pyBigWig.__file__))
exit(1)
old_chrom = chrom_list[0]
header = []
for i, _chrom in enumerate(chrom_list):
if old_chrom != _chrom:
header.append((toString(old_chrom), end_list[i - 1]))
old_chrom = _chrom
header.append((toString(chrom_list[-1]), end_list[-1]))
for idx, outfile in enumerate(args.outputFileName):
log.debug("bigwig: len(vecs_list) {}".format(len(vecs_list)))
log.debug("bigwig: len(chrom_list) {}".format(len(chrom_list)))
assert (len(vecs_list) == len(chrom_list))
_chrom_list = []
_start_list = []
_end_list = []
values = []
bw = pyBigWig.open(outfile, 'w')
# set big wig header
bw.addHeader(header)
# create entry lists
for i, value in enumerate(vecs_list):
# it can happen that some 'value' is having less dimensions than it should
if len(value) == args.numberOfEigenvectors:
if isinstance(value[idx], np.complex):
value[idx] = value[idx].real
values.append(value[idx])
_chrom_list.append(toString(chrom_list[i]))
_start_list.append(start_list[i])
_end_list.append(end_list[i])
# write entries
bw.addEntries(_chrom_list,
_start_list,
ends=_end_list,
values=values)
bw.close()
else:
log.error("Output format not known: {}".format(args.format))
exit(1)
def main(args=None):
args = parse_arguments().parse_args(args)
if args.verbose:
log.setLevel(logging.INFO)
# args.chromosomes
if check_cooler(args.matrix) and args.chromosomes is not None and len(
args.chromosomes) == 1:
ma = hm.hiCMatrix(args.matrix, pChrnameList=toString(args.chromosomes))
else:
ma = hm.hiCMatrix(args.matrix)
if args.chromosomes:
ma.reorderChromosomes(toString(args.chromosomes))
# mask all zero value bins
if 'correctionMethod' in args:
if args.correctionMethod == 'ICE':
row_sum = np.asarray(ma.matrix.sum(axis=1)).flatten()
log.info("Removing {} zero value bins".format(sum(row_sum == 0)))
ma.maskBins(np.flatnonzero(row_sum == 0))
matrix_shape = ma.matrix.shape
if 'plotName' in args:
row_sum = np.asarray(ma.matrix.sum(axis=1)).flatten()
log.info("Removing {} zero value bins".format(sum(row_sum == 0)))
ma.maskBins(np.flatnonzero(row_sum == 0))
matrix_shape = ma.matrix.shape
ma.matrix = convertNansToZeros(ma.matrix)
ma.matrix = convertInfsToZeros(ma.matrix)
ma.matrix = ma.matrix.astype(np.float64, copy=True)
log.debug('ma.matrix.indices {}'.format(ma.matrix.indices.dtype))
log.debug('ma.matrix.data {}'.format(ma.matrix.data.dtype))
log.debug('ma.matrix.indptr {}'.format(ma.matrix.indptr.dtype))
# log.debug('ma.matrix.indices {}'.format(np.max(ma.matrix.indices)))
# log.debug('ma.matrix.data {}'.format(np.max(ma.matrix.data)))
# log.debug('ma.matrix.indptr {}'.format(np.max(ma.matrix.indptr)))
# ma.matrix.indptr = ma.matrix.indptr.astype(np.int32, copy=False)
# ma.matrix.indices = ma.matrix.indices.astype(np.int32, copy=False)
if 'plotName' in args:
plot_total_contact_dist(ma, args)
log.info("Saving diagnostic plot {}\n".format(args.plotName))
return
log.info("matrix contains {} data points. Sparsity {:.3f}.".format(
len(ma.matrix.data),
float(len(ma.matrix.data)) / (ma.matrix.shape[0]**2)))
if args.skipDiagonal:
ma.diagflat(value=0)
total_filtered_out = set()
if args.correctionMethod == 'ICE':
if not args.filterThreshold:
log.error('min and max filtering thresholds should be set')
sys.exit(1)
outlier_regions = filter_by_zscore(ma,
args.filterThreshold[0],
args.filterThreshold[1],
perchr=args.perchr)
# compute and print some statistics
pct_outlier = 100 * float(len(outlier_regions)) / ma.matrix.shape[0]
ma.printchrtoremove(outlier_regions,
label="Bins that are MAD outliers ({:.2f}%) "
"out of".format(pct_outlier, ma.matrix.shape[0]),
restore_masked_bins=False)
assert matrix_shape == ma.matrix.shape
# mask filtered regions
ma.maskBins(outlier_regions)
total_filtered_out = set(outlier_regions)
if args.sequencedCountCutoff and 0 < args.sequencedCountCutoff < 1:
chrom, _, _, coverage = zip(*ma.cut_intervals)
assert type(coverage[0]) == np.float64
failed_bins = np.flatnonzero(
np.array(coverage) < args.sequencedCountCutoff)
ma.printchrtoremove(failed_bins,
label="Bins with low coverage",
restore_masked_bins=False)
ma.maskBins(failed_bins)
total_filtered_out = set(failed_bins)
"""
ma.matrix, to_remove = fill_gaps(ma, failed_bins)
log.warning("From {} failed bins, {} could "
"not be filled\n".format(len(failed_bins),
len(to_remove)))
ma.maskBins(to_remove)
"""
if args.transCutoff and 0 < args.transCutoff < 100:
cutoff = float(args.transCutoff) / 100
# a usual cutoff is 0.05
ma.truncTrans(high=cutoff)
pre_row_sum = np.asarray(ma.matrix.sum(axis=1)).flatten()
correction_factors = []
corrected_matrix = lil_matrix(ma.matrix.shape)
if args.perchr:
# normalize each chromosome independently
for chrname in list(ma.interval_trees):
chr_range = ma.getChrBinRange(chrname)
chr_submatrix = ma.matrix[chr_range[0]:chr_range[1],
chr_range[0]:chr_range[1]]
if args.correctionMethod == 'ICE':
_matrix, _corr_factors = iterative_correction(
chr_submatrix, args)
corrected_matrix[chr_range[0]:chr_range[1],
chr_range[0]:chr_range[1]] = _matrix
correction_factors.append(_corr_factors)
else:
# Set the kr matrix along with its correction factors vector
assert (args.correctionMethod == 'KR')
log.debug("Loading a float sparse matrix for KR balancing")
kr = kr_balancing(
chr_submatrix.shape[0], chr_submatrix.shape[1],
chr_submatrix.count_nonzero(),
chr_submatrix.indptr.astype(np.int64, copy=False),
chr_submatrix.indices.astype(np.int64, copy=False),
chr_submatrix.data.astype(np.float64, copy=False))
kr.computeKR()
if args.outFileName.endswith('.h5'):
corrected_matrix[
chr_range[0]:chr_range[1],
chr_range[0]:chr_range[1]] = kr.get_normalised_matrix(
True)
# correction_factors.append(np.true_divide(1,
# kr.get_normalisation_vector(False).todense()))
correction_factors.append(
kr.get_normalisation_vector(False).todense())
correction_factors = np.concatenate(correction_factors)
else:
if args.correctionMethod == 'ICE':
corrected_matrix, correction_factors = iterative_correction(
ma.matrix, args)
ma.setMatrixValues(corrected_matrix)
else:
assert (args.correctionMethod == 'KR')
log.debug("Loading a float sparse matrix for KR balancing")
kr = kr_balancing(ma.matrix.shape[0], ma.matrix.shape[1],
ma.matrix.count_nonzero(),
ma.matrix.indptr.astype(np.int64, copy=False),
ma.matrix.indices.astype(np.int64, copy=False),
ma.matrix.data.astype(np.float64, copy=False))
log.debug('passed pointers')
kr.computeKR()
log.debug('computation done')
# set it to False since the vector is already normalised
# with the previous True
# correction_factors = np.true_divide(1, kr.get_normalisation_vector(False).todense())
correction_factors = kr.get_normalisation_vector(False).todense()
if args.outFileName.endswith('.h5'):
corrected_matrix = kr.get_normalised_matrix(True)
if args.outFileName.endswith('.h5'):
ma.setMatrixValues(corrected_matrix)
# if
ma.setCorrectionFactors(correction_factors)
log.debug("Correction factors {}".format(correction_factors[:10]))
if args.inflationCutoff and args.inflationCutoff > 0 and args.correctionMethod == 'ICE':
after_row_sum = np.asarray(corrected_matrix.sum(axis=1)).flatten()
# identify rows that were expanded more than args.inflationCutoff times
to_remove = np.flatnonzero(
after_row_sum / pre_row_sum >= args.inflationCutoff)
ma.printchrtoremove(to_remove,
label="inflated >={} "
"regions".format(args.inflationCutoff),
restore_masked_bins=False)
total_filtered_out = total_filtered_out.union(to_remove)
ma.maskBins(to_remove)
ma.printchrtoremove(sorted(list(total_filtered_out)),
label="Total regions to be removed",
restore_masked_bins=False)
ma.save(args.outFileName, pApplyCorrection=False)
def plot_total_contact_dist(hic_ma, args):
"""
Plots the distribution of number of contacts (excluding self contacts)
Outliers with a high number are removed for the plot
:param hic_ma: sparse matrix
:return:
"""
use('Agg')
majorlocator = MultipleLocator(1)
majorformatter = FormatStrFormatter('%d')
minorlocator = MultipleLocator(0.2)
def plot_histogram(row_sum_values, mad_values, ax1, title=None):
if args.xMax:
ax1.set_xlim(ax1.get_xlim()[0], args.xMax)
row_sum_values = row_sum_values[row_sum_values < args.xMax]
ax1.set_xlabel("total counts per bin")
ax1.set_ylabel("frequency")
# ax1.xaxis.grid(True)
ax1.patch.set_visible(False)
dist, bin_s, __ = ax1.hist(row_sum_values, 100, color='green')
# add second axis on top
ax2 = ax1.twiny()
ax2.set_xlabel("modified z-score")
ax2.xaxis.set_major_locator(majorlocator)
ax2.xaxis.set_major_formatter(majorformatter)
ax2.xaxis.grid(True, which='minor')
# for the minor ticks, use no labels; default NullFormatter
ax2.xaxis.set_minor_locator(minorlocator)
# update second axis values by mapping the min max
# of the main axis to the translated values
# into modified z score.
# workaround for 'Axis limits cannot be NaN or Inf' bug in version 2.1.1
log.debug("ax1.get_xlim(): {}".format(ax1.get_xlim()))
log.debug("np.array(ax1.get_xlim()): {}".format(
np.array(ax1.get_xlim())))
log.debug(
"mad_values.value_to_mad(np.array(ax1.get_xlim())): {}".format(
mad_values.value_to_mad(np.array(ax1.get_xlim()))))
ax2.set_xlim(mad_values.value_to_mad(np.array(ax1.get_xlim())))
# get first local mininum value
local_min = [
x for x, y in enumerate(dist)
if 1 <= x < len(dist) - 1 and dist[x - 1] > y < dist[x + 1]
]
if len(local_min) > 0:
threshold = bin_s[local_min[0]]
else:
threshold = None
if threshold:
mad_threshold = mad_values.value_to_mad(threshold)
ymin, ymax = ax2.get_ylim()
ax2.vlines(mad_threshold, ymin, ymax)
if title:
log.info("{}: mad threshold {}".format(title, mad_threshold))
else:
log.info("mad threshold {}".format(mad_threshold))
# replace nan by 0
# hic_ma.matrix.data[np.isnan(hic_ma.matrix.data)] = 0
hic_ma.matrix = convertNansToZeros(hic_ma.matrix)
hic_ma.matrix = convertInfsToZeros(hic_ma.matrix)
if args.perchr:
chroms = hic_ma.getChrNames()
if len(chroms) > 30:
log.warning("The matrix contains {} chromosomes. It is not "
"practical to plot each. Try using --chromosomes to "
"select some chromosomes or plot a single histogram.")
num_rows = int(np.ceil(float(len(chroms)) / 5))
num_cols = min(len(chroms), 5)
grids = gridspec.GridSpec(num_rows, num_cols)
fig = plt.figure(figsize=(6 * num_cols, 5 * num_rows))
ax = {}
for plot_num, chrname in enumerate(chroms):
log.info("Plotting chromosome {}".format(chrname))
chr_range = hic_ma.getChrBinRange(chrname)
chr_submatrix = hic_ma.matrix[chr_range[0]:chr_range[1],
chr_range[0]:chr_range[1]]
row_sum = np.asarray(chr_submatrix.sum(axis=1)).flatten()
row_sum = row_sum - chr_submatrix.diagonal()
mad = MAD(row_sum)
modified_z_score = mad.get_motified_zscores()
# high remove outliers
row_sum = row_sum[modified_z_score < 5]
col = plot_num % num_cols
row = plot_num // num_cols
ax[chrname] = fig.add_subplot(grids[row, col])
plot_histogram(row_sum, mad, ax[chrname], title=chrname)
ax[chrname].set_title(chrname)
else:
fig = plt.figure()
row_sum = np.asarray(hic_ma.matrix.sum(axis=1)).flatten()
row_sum = row_sum - hic_ma.matrix.diagonal()
mad = MAD(row_sum)
modified_z_score = mad.get_motified_zscores()
# high remove outliers
row_sum = row_sum[modified_z_score < 5]
ax = fig.add_subplot(111)
plot_histogram(row_sum, mad, ax)
plt.tight_layout()
plt.savefig(args.plotName)
plt.close()
def main(args=None):
args = parse_arguments().parse_args(args)
if int(args.numberOfEigenvectors) != len(args.outputFileName):
log.error(
"Number of output file names and number of eigenvectors does not match. Please"
"provide the name of each file.\nFiles: {}\nNumber of eigenvectors: {}"
.format(args.outputFileName, args.numberOfEigenvectors))
exit(1)
ma = hm.hiCMatrix(args.matrix)
ma.maskBins(ma.nan_bins)
if args.chromosomes:
ma.keepOnlyTheseChr(args.chromosomes)
vecs_list = []
chrom_list = []
start_list = []
end_list = []
# PCA is computed per chromosome
length_chromosome = 0
chromosome_count = len(ma.getChrNames())
for chrname in ma.getChrNames():
chr_range = ma.getChrBinRange(chrname)
length_chromosome += chr_range[1] - chr_range[0]
for chrname in ma.getChrNames():
chr_range = ma.getChrBinRange(chrname)
log.debug("Computing pca for chromosome: {}".format(chrname))
submatrix = ma.matrix[chr_range[0]:chr_range[1],
chr_range[0]:chr_range[1]]
exp_obs_matrix_ = exp_obs_matrix_lieberman(submatrix,
length_chromosome,
chromosome_count)
exp_obs_matrix_ = convertNansToZeros(
csr_matrix(exp_obs_matrix_)).todense()
exp_obs_matrix_ = convertInfsToZeros(
csr_matrix(exp_obs_matrix_)).todense()
pearson_correlation_matrix = np.corrcoef(exp_obs_matrix_)
pearson_correlation_matrix = convertNansToZeros(
csr_matrix(pearson_correlation_matrix)).todense()
pearson_correlation_matrix = convertInfsToZeros(
csr_matrix(pearson_correlation_matrix)).todense()
corrmatrix = np.cov(pearson_correlation_matrix)
corrmatrix = convertNansToZeros(csr_matrix(corrmatrix)).todense()
corrmatrix = convertInfsToZeros(csr_matrix(corrmatrix)).todense()
evals, eigs = linalg.eig(corrmatrix)
k = args.numberOfEigenvectors
chrom, start, end, _ = zip(
*ma.cut_intervals[chr_range[0]:chr_range[1]])
vecs_list += eigs[:, :k].tolist()
chrom_list += chrom
start_list += start
end_list += end
if args.format == 'bedgraph':
for idx, outfile in enumerate(args.outputFileName):
assert (len(vecs_list) == len(chrom_list))
with open(outfile, 'w') as fh:
for i, value in enumerate(vecs_list):
if len(value) == args.numberOfEigenvectors:
if isinstance(value[idx], np.complex):
value[idx] = value[idx].real
fh.write("{}\t{}\t{}\t{:.12f}\n".format(
toString(chrom_list[i]), start_list[i],
end_list[i], value[idx]))
elif args.format == 'bigwig':
if not pyBigWig.numpy == 1:
log.error(
"ERROR: Your version of pyBigWig is not supporting numpy: {}".
format(pyBigWig.__file__))
exit(1)
old_chrom = chrom_list[0]
header = []
for i, chrom_ in enumerate(chrom_list):
if old_chrom != chrom_:
header.append((toString(old_chrom), end_list[i - 1]))
old_chrom = chrom_
header.append((toString(chrom_list[-1]), end_list[-1]))
for idx, outfile in enumerate(args.outputFileName):
log.debug("bigwig: len(vecs_list) {}".format(len(vecs_list)))
log.debug("bigwig: len(chrom_list) {}".format(len(chrom_list)))
assert (len(vecs_list) == len(chrom_list))
chrom_list_ = []
start_list_ = []
end_list_ = []
values = []
bw = pyBigWig.open(outfile, 'w')
# set big wig header
bw.addHeader(header)
# create entry lists
for i, value in enumerate(vecs_list):
# it can happen that some 'value' is having less dimensions than it should
if len(value) == args.numberOfEigenvectors:
if isinstance(value[idx], np.complex):
value[idx] = value[idx].real
values.append(value[idx])
chrom_list_.append(toString(chrom_list[i]))
start_list_.append(start_list[i])
end_list_.append(end_list[i])
# write entries
bw.addEntries(chrom_list_,
start_list_,
ends=end_list_,
values=values)
bw.close()
else:
log.error("Output format not known: {}".format(args.format))
exit(1)
def _obs_exp_non_zero(pSubmatrix):
obs_exp_matrix_ = obs_exp_matrix_non_zero(pSubmatrix)
obs_exp_matrix_ = convertNansToZeros(csr_matrix(obs_exp_matrix_))
obs_exp_matrix_ = convertInfsToZeros(csr_matrix(obs_exp_matrix_)).todense()
return obs_exp_matrix_
def main(args=None):
args = parse_arguments().parse_args(args)
if args.verbose:
log.setLevel(logging.INFO)
# args.chromosomes
if check_cooler(args.matrix) and args.chromosomes is not None and len(args.chromosomes) == 1:
ma = hm.hiCMatrix(args.matrix, pChrnameList=toString(args.chromosomes))
else:
ma = hm.hiCMatrix(args.matrix)
if args.chromosomes:
ma.reorderChromosomes(toString(args.chromosomes))
# mask all zero value bins
row_sum = np.asarray(ma.matrix.sum(axis=1)).flatten()
log.info("Removing {} zero value bins".format(sum(row_sum == 0)))
ma.maskBins(np.flatnonzero(row_sum == 0))
matrix_shape = ma.matrix.shape
ma.matrix = convertNansToZeros(ma.matrix)
ma.matrix = convertInfsToZeros(ma.matrix)
if 'plotName' in args:
plot_total_contact_dist(ma, args)
log.info("Saving diagnostic plot {}\n".format(args.plotName))
return
log.info("matrix contains {} data points. Sparsity {:.3f}.".format(
len(ma.matrix.data),
float(len(ma.matrix.data)) / (ma.matrix.shape[0] ** 2)))
if args.skipDiagonal:
ma.diagflat(value=0)
outlier_regions = filter_by_zscore(ma, args.filterThreshold[0], args.filterThreshold[1], perchr=args.perchr)
# compute and print some statistics
pct_outlier = 100 * float(len(outlier_regions)) / ma.matrix.shape[0]
ma.printchrtoremove(outlier_regions, label="Bins that are MAD outliers ({:.2f}%) "
"out of".format(pct_outlier, ma.matrix.shape[0]),
restore_masked_bins=False)
assert matrix_shape == ma.matrix.shape
# mask filtered regions
ma.maskBins(outlier_regions)
total_filtered_out = set(outlier_regions)
if args.sequencedCountCutoff and 0 < args.sequencedCountCutoff < 1:
chrom, _, _, coverage = zip(*ma.cut_intervals)
assert type(coverage[0]) == np.float64
failed_bins = np.flatnonzero(
np.array(coverage) < args.sequencedCountCutoff)
ma.printchrtoremove(failed_bins, label="Bins with low coverage", restore_masked_bins=False)
ma.maskBins(failed_bins)
total_filtered_out = set(failed_bins)
"""
ma.matrix, to_remove = fill_gaps(ma, failed_bins)
log.warning("From {} failed bins, {} could "
"not be filled\n".format(len(failed_bins),
len(to_remove)))
ma.maskBins(to_remove)
"""
if args.transCutoff and 0 < args.transCutoff < 100:
cutoff = float(args.transCutoff) / 100
# a usual cutoff is 0.05
ma.truncTrans(high=cutoff)
pre_row_sum = np.asarray(ma.matrix.sum(axis=1)).flatten()
correction_factors = []
if args.perchr:
corrected_matrix = lil_matrix(ma.matrix.shape)
# normalize each chromosome independently
for chrname in list(ma.interval_trees):
chr_range = ma.getChrBinRange(chrname)
chr_submatrix = ma.matrix[chr_range[0]:chr_range[1], chr_range[0]:chr_range[1]]
_matrix, _corr_factors = iterative_correction(chr_submatrix, args)
corrected_matrix[chr_range[0]:chr_range[1], chr_range[0]:chr_range[1]] = _matrix
correction_factors.append(_corr_factors)
correction_factors = np.concatenate(correction_factors)
else:
corrected_matrix, correction_factors = iterative_correction(ma.matrix, args)
ma.setMatrixValues(corrected_matrix)
ma.setCorrectionFactors(correction_factors)
log.info("Correction factors {}".format(correction_factors[:10]))
if args.inflationCutoff and args.inflationCutoff > 0:
after_row_sum = np.asarray(corrected_matrix.sum(axis=1)).flatten()
# identify rows that were expanded more than args.inflationCutoff times
to_remove = np.flatnonzero(after_row_sum / pre_row_sum >= args.inflationCutoff)
ma.printchrtoremove(to_remove,
label="inflated >={} "
"regions".format(args.inflationCutoff), restore_masked_bins=False)
total_filtered_out = total_filtered_out.union(to_remove)
ma.maskBins(to_remove)
ma.printchrtoremove(sorted(list(total_filtered_out)),
label="Total regions to be removed", restore_masked_bins=False)
ma.save(args.outFileName, pApplyCorrection=False)
def open_and_store_matrix(pMatrixName, pMatricesList, pIndex, pXDimension,
pChromosomes, pNorm, pExtraTrack, pHistonMarkType,
pBinarization, pQueue):
compartments_matrix = None
for i, matrix in enumerate(pMatricesList):
ma = hm.hiCMatrix(pMatrixName + '::' + matrix)
# WARNING
# DO NOT APPLY BIN MASKING, WILL LEAD TO DIFFERENT SIZES OF THE CHROMOSOMES
# THIS IS CAUSING A FAIL OF THE COMPUTATION
# ma.maskBins(ma.nan_bins)
k = 1
if pChromosomes:
ma.keepOnlyTheseChr(pChromosomes)
vecs_list = []
chrom_list = []
start_list = []
end_list = []
# PCA is computed per chromosome
length_chromosome = 0
chromosome_count = len(ma.getChrNames())
for chrname in ma.getChrNames():
chr_range = ma.getChrBinRange(chrname)
length_chromosome += chr_range[1] - chr_range[0]
if pExtraTrack and (pExtraTrack.endswith('.bw')
or pExtraTrack.endswith('.bigwig')):
bwTrack = pyBigWig.open(pExtraTrack, 'r')
for chrname in ma.getChrNames():
chr_range = ma.getChrBinRange(chrname)
submatrix = ma.matrix[chr_range[0]:chr_range[1],
chr_range[0]:chr_range[1]]
if pNorm:
obs_exp_matrix_ = obs_exp_matrix_norm(submatrix)
else:
obs_exp_matrix_ = obs_exp_matrix_lieberman(
submatrix, length_chromosome, chromosome_count)
obs_exp_matrix_ = convertNansToZeros(
csr_matrix(obs_exp_matrix_)).todense()
obs_exp_matrix_ = convertInfsToZeros(
csr_matrix(obs_exp_matrix_)).todense()
pearson_correlation_matrix = np.corrcoef(obs_exp_matrix_)
pearson_correlation_matrix = convertNansToZeros(
csr_matrix(pearson_correlation_matrix)).todense()
pearson_correlation_matrix = convertInfsToZeros(
csr_matrix(pearson_correlation_matrix)).todense()
corrmatrix = np.cov(pearson_correlation_matrix)
corrmatrix = convertNansToZeros(csr_matrix(corrmatrix)).todense()
corrmatrix = convertInfsToZeros(csr_matrix(corrmatrix)).todense()
evals, eigs = linalg.eig(corrmatrix)
chrom, start, end, _ = zip(
*ma.cut_intervals[chr_range[0]:chr_range[1]])
chrom_list += chrom
start_list += start
end_list += end
if pExtraTrack and (pExtraTrack.endswith('.bw')
or pExtraTrack.endswith('.bigwig')):
assert (len(end) == len(start))
correlateEigenvectorWithHistonMarkTrack(
eigs[:, :k].transpose(), bwTrack, chrname, start, end,
pExtraTrack, pHistonMarkType)
vecs_list += eigs[:, :k].tolist()
if compartments_matrix is None:
compartments_matrix = np.zeros(
[pXDimension, len(np.array(vecs_list).flatten())],
dtype=np.float)
eigenvector = np.real(np.array(vecs_list).flatten())
mask = np.isnan(eigenvector)
if len(mask) > 0:
eigenvector[mask] = 0
mask = np.isinf(eigenvector)
if len(mask) > 0:
eigenvector[mask] = 0
if pBinarization:
mask = eigenvector <= 0
eigenvector[mask] = -1
mask = eigenvector > 0
eigenvector[mask] = 1
compartments_matrix[pIndex + i, :] = eigenvector
pQueue.put(compartments_matrix)
return