def main():
args = parse_arguments().parse_args()
for matrix in args.matrices:
# if
hic_ma = hm.hiCMatrix(matrix)
size = hic_ma.matrix.shape[0]
num_non_zero = hic_ma.matrix.nnz
sum_elements = hic_ma.matrix.sum() / 2
bin_length = hic_ma.getBinSize()
num_nan_bins = len(hic_ma.nan_bins)
min_non_zero = hic_ma.matrix.data.min()
max_non_zero = hic_ma.matrix.data.max()
chromosomes = list(hic_ma.chrBinBoundaries)
if args.outFileName:
with open(args.outFileName, 'w') as file:
file.write(
"# Matrix information file. Created with HiCExplorer's hicInfo version {}\n"
.format(__version__))
file.write("File:\t{}\n".format(matrix))
file.write("Size:\t{:,}\n".format(size))
file.write("Sum:\t{:,}\n".format(sum_elements))
file.write("Bin_length:\t{}\n".format(bin_length))
file.write("Chromosomes:\t{}\n".format(", ".join(
toString(chromosomes))))
file.write("Non-zero elements:\t{:,}\n".format(num_non_zero))
file.write("Minimum (non zero):\t{}\n".format(min_non_zero))
file.write("Maximum:\t{}\n".format(max_non_zero))
file.write("NaN bins:\t{}\n".format(num_nan_bins))
if check_cooler(matrix):
file.write(
'The following columns are available: {}'.format(
hic_ma.getInformationCoolerBinNames()))
else:
print("File:\t{}".format(matrix))
print("Size:\t{:,}".format(size))
print("Sum:\t{:,}".format(sum_elements))
print("Bin_length:\t{}".format(bin_length))
print("Chromosomes:\t{}".format(", ".join(toString(chromosomes))))
print("Non-zero elements:\t{:,}".format(num_non_zero))
print("Minimum (non zero):\t{}".format(min_non_zero))
print("Maximum:\t{}".format(max_non_zero))
print("NaN bins:\t{}".format(num_nan_bins))
if check_cooler(matrix):
print('The following columns are available: {}'.format(
hic_ma.getInformationCoolerBinNames()))
def main():
args = parse_arguments().parse_args()
for matrix in args.matrices:
# if
hic_ma = hm.hiCMatrix(matrix)
size = hic_ma.matrix.shape[0]
num_non_zero = hic_ma.matrix.nnz
sum_elements = hic_ma.matrix.sum() / 2
bin_length = hic_ma.getBinSize()
num_nan_bins = len(hic_ma.nan_bins)
min_non_zero = hic_ma.matrix.data.min()
max_non_zero = hic_ma.matrix.data.max()
chromosomes = list(hic_ma.chrBinBoundaries)
print("File:\t{}".format(matrix))
print("Size:\t{:,}".format(size))
print("Sum:\t{:,}".format(sum_elements))
print("Bin_length:\t{}".format(bin_length))
print("Chromosomes:\t{}".format(", ".join(toString(chromosomes))))
print("Non-zero elements:\t{:,}".format(num_non_zero))
print("Minimum (non zero):\t{}".format(min_non_zero))
print("Maximum:\t{}".format(max_non_zero))
print("NaN bins:\t{}".format(num_nan_bins))
if check_cooler(matrix):
hic_ma.getInformationCoolerBinNames()
def adjustMatrix(pArgs):
if pArgs.chromosomes is not None and pArgs.regions is not None:
log.error('Please specify either --chromosomes or --regions.')
exit(1)
hic_matrix = None
if pArgs.chromosomes:
if check_cooler(pArgs.matrix) and len(pArgs.chromosomes) == 1 and pArgs.action == 'keep':
chromosomes_list = cooler.Cooler(pArgs.matrix).chromnames
if pArgs.chromosomes[0] in chromosomes_list:
hic_matrix = hm.hiCMatrix(pArgs.matrix, pChrnameList=pArgs.chromosomes)
else:
log.error('Chromosome not available in matrix: {} {}'.format(pArgs.matrix, pArgs.chromosomes[0]))
exit(1)
else:
hic_matrix = hm.hiCMatrix(pArgs.matrix)
chromosomes_list = list(hic_matrix.chrBinBoundaries)
chromosomes_list_to_operate_on = []
for chromosome in pArgs.chromosomes:
if chromosome in chromosomes_list:
chromosomes_list_to_operate_on.append(chromosome)
else:
log.warning('Chromosome not available in matrix: {} {}'.format(pArgs.matrix, chromosome))
if len(chromosomes_list_to_operate_on) == 0:
log.error('No valid chromosome given: {}. Available: {}'.format(pArgs.chromosomes, chromosomes_list))
exit(1)
if pArgs.action == 'keep':
hic_matrix.reorderChromosomes(chromosomes_list_to_operate_on)
elif pArgs.action == 'remove':
for chromosome in chromosomes_list:
if chromosome in chromosomes_list_to_operate_on:
chromosomes_list.remove(chromosome)
hic_matrix.reorderChromosomes(chromosomes_list)
elif pArgs.action == 'mask':
hic_matrix.maskChromosomes(chromosomes_list_to_operate_on)
elif pArgs.regions:
hic_matrix = hm.hiCMatrix(pArgs.matrix)
chromosomes_list = list(hic_matrix.chrBinBoundaries)
genomic_regions = []
with open(pArgs.regions, 'r') as file:
for line in file.readlines():
_line = line.strip().split('\t')
log.debug('_line {}'.format(_line))
if len(line) < 3:
log.warning("An entry shorter than 3 columns has been found!")
continue
if len(_line) >= 3:
chrom, start, end = _line[0], int(_line[1]), int(_line[2])
log.debug('chrom {}'.format(chrom))
if chrom in chromosomes_list:
genomic_regions.append((chrom, start, end))
else:
log.warning('Chromosome not available in matrix, '
'ignoring regions: {} {}'.format(pArgs.matrix, chrom))
if len(genomic_regions) == 0:
log.error('No valid chromosome given. Available: {}'.format(chromosomes_list))
exit(1)
matrix_indices_regions = []
for region in genomic_regions:
log.debug('region {}'.format(region))
_regionBinRange = hic_matrix.getRegionBinRange(region[0], int(region[1]), int(region[2]))
if _regionBinRange is not None:
start, end = _regionBinRange
matrix_indices_regions.extend(list(range(start, end + 1))) # end is inclusive, so +1
if pArgs.action == 'remove':
chr_start, chr_end = hic_matrix.getChrBinRange(chrom)
if (start > chr_start) and (end < chr_end - 1):
log.warning("{}:{}-{} entry may generate discounted regions on a chromosome."
"Please consider using `mask` action to deal with that.".format(chrom, start, end))
if pArgs.action == 'keep':
hic_matrix.reorderBins(matrix_indices_regions)
elif pArgs.action == 'mask':
hic_matrix.maskBins(matrix_indices_regions)
elif pArgs.action == 'remove':
hic_matrix.maskBins(matrix_indices_regions)
hic_matrix.orig_bin_ids = []
hic_matrix.orig_cut_intervals = []
hic_matrix.nan_bins = []
elif pArgs.maskBadRegions:
if check_cooler(pArgs.matrix) and len(pArgs.chromosomes) == 1 and pArgs.action == 'keep':
hic_matrix = hm.hiCMatrix(pArgs.matrix, pChrnameList=pArgs.chromosomes)
else:
hic_matrix = hm.hiCMatrix(pArgs.matrix)
else:
log.info('No data to adjust given. Please specify either --chromosomes or --region parameter.')
return hic_matrix
def main(args=None):
args = parse_arguments().parse_args(args)
if args.chromosomes is not None and args.regions is not None:
log.error('Please specify either --chromosomes or --regions.')
exit(1)
hic_ma = None
if args.chromosomes:
if check_cooler(args.matrix) and len(
args.chromosomes) == 1 and args.action == 'keep':
hic_ma = hm.hiCMatrix(args.matrix, pChrnameList=args.chromosomes)
else:
hic_ma = hm.hiCMatrix(args.matrix)
if args.action == 'keep':
hic_ma.reorderChromosomes(args.chromosomes)
elif args.action == 'remove':
chromosomes = list(hic_ma.chrBinBoundaries)
for chromosome in args.chromosomes:
if chromosome in chromosomes:
chromosomes.remove(chromosome)
hic_ma.reorderChromosomes(chromosomes)
elif args.action == 'mask':
hic_ma.maskChromosomes(args.chromosomes)
elif args.regions:
hic_ma = hm.hiCMatrix(args.matrix)
genomic_regions = []
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) == 3:
chrom, start, end = _line[0], _line[1], int(_line[2]) - 1
genomic_regions.append((chrom, start, end))
# log.debug('genomic_regions {}'.format(genomic_regions))
matrix_indices_regions = []
for region in genomic_regions:
_regionBinRange = hic_ma.getRegionBinRange(region[0], region[1],
region[2])
if _regionBinRange is not None:
start, end = _regionBinRange
matrix_indices_regions.extend(list(range(start, end)))
# log.debug('matrix_indices_regions {}'.format(matrix_indices_regions))
if args.action == 'keep':
hic_ma.reorderBins(matrix_indices_regions)
elif args.action == 'mask':
hic_ma.maskBins(matrix_indices_regions)
elif args.action == 'remove':
full_matrix_range = np.array(
range(0, max(hic_ma.matrix.shape[0], hic_ma.matrix.shape[1])))
matrix_indices_regions = np.array(matrix_indices_regions)
full_matrix_range[matrix_indices_regions] = -1
mask = full_matrix_range != -1
full_matrix_range = full_matrix_range[mask]
hic_ma.reorderBins(full_matrix_range)
else:
log.info(
'No data to adjust given. Please specify either --chromosomes or --region parameter.'
)
if hic_ma is not None:
hic_ma.save(args.outFileName)
def main(args=None):
args = parse_arguments().parse_args(args)
short_v_long_range = []
sum_smaller = []
sum_greater = []
for matrix in args.matrices:
is_cooler = check_cooler(matrix)
if not is_cooler:
hic_matrix = hm.hiCMatrix(matrix)
else:
hic_matrix = matrix
if args.chromosomes is None:
# get all chromosomes from cooler file
if not is_cooler:
chromosomes_list = list(hic_matrix.chrBinBoundaries)
else:
chromosomes_list = cooler.Cooler(matrix).chromnames
else:
chromosomes_list = args.chromosomes
short_v_long_range_matrix_threads = [None] * args.threads
sum_smaller_threads = [None] * args.threads
sum_greater_threads = [None] * args.threads
chromosomesListPerThread = len(chromosomes_list) // args.threads
all_data_collected = False
queue = [None] * args.threads
process = [None] * args.threads
thread_done = [False] * args.threads
for i in range(args.threads):
if i < args.threads - 1:
chromosomeListThread = chromosomes_list[
i * chromosomesListPerThread:(i + 1) *
chromosomesListPerThread]
else:
chromosomeListThread = chromosomes_list[
i * chromosomesListPerThread:]
queue[i] = Queue()
process[i] = Process(target=compute_relation_short_long_range,
kwargs=dict(pHiCMatrix=hic_matrix,
pChromosomes=chromosomeListThread,
pDistance=args.distance,
pIsCooler=is_cooler,
pQueue=queue[i]))
process[i].start()
while not all_data_collected:
for i in range(args.threads):
if queue[i] is not None and not queue[i].empty():
short_v_long_range_matrix_threads[i], sum_smaller_threads[
i], sum_greater_threads[i] = queue[i].get()
queue[i] = None
process[i].join()
process[i].terminate()
process[i] = None
thread_done[i] = True
all_data_collected = True
for thread in thread_done:
if not thread:
all_data_collected = False
time.sleep(1)
short_v_long_range_matrix = [
item for sublist in short_v_long_range_matrix_threads
for item in sublist
]
sum_smaller_matrix = [
item for sublist in sum_smaller_threads for item in sublist
]
sum_greater_matrix = [
item for sublist in sum_greater_threads for item in sublist
]
short_v_long_range.append(short_v_long_range_matrix)
sum_smaller.append(sum_smaller_matrix)
sum_greater.append(sum_greater_matrix)
log.debug(short_v_long_range)
plt.ylabel('Sum short range / long range')
plt.tick_params(axis='x',
which='both',
bottom=False,
top=False,
labelbottom=False)
box_plot = plt.boxplot(short_v_long_range, patch_artist=True)
legend_handels_color = []
for i, patch in enumerate(box_plot['boxes']):
patch.set_facecolor(args.colorList[i % len(args.colorList)])
legend_handels_color.append(
mpatches.Patch(color=args.colorList[i % len(args.colorList)],
label=args.matrices[i].split('/')[-1]))
plt.legend(handles=legend_handels_color)
plt.xlabel('Boxplot shows svl-ratio per chromosome.')
plt.savefig(args.plotFileName, dpi=args.dpi)
if len(args.matrices) > 1:
p_values = []
for i, sample in enumerate(short_v_long_range):
for sample2 in short_v_long_range[i + 1:]:
statistic, significance_level = ranksums(sample, sample2)
p_values.append(significance_level)
log.debug('p_values {}'.format(p_values))
with open(args.outFileName, 'w') as file:
header = '# Created with HiCExplorer\'s hicPlotSVL ' + __version__ + '\n'
header += "# Short range vs long range contacts per chromosome, p-values of each distribution against each other distribution with Wilcoxon rank-sum\n"
header += '# Short range contacts: <= ' + str(args.distance) + '\n'
file.write(header)
counter = 0
for i, matrix_0 in enumerate(args.matrices):
for j, matrix_1 in enumerate(args.matrices[i + 1:]):
file.write(matrix_0 + '\t' + matrix_1 + '\t' +
str(p_values[counter]) + '\n')
counter += 1
with open(args.outFileNameData, 'w') as file:
header = '# Created with HiCExplorer\'s hicPlotSVL ' + __version__ + '\n'
header += "# Short range vs long range contacts per chromosome: raw data\n"
header += '# Short range contacts: <= ' + str(args.distance) + '\n'
matrices_names = '\t\t\t'.join(args.matrices)
header += '#\t{}\n'.format(matrices_names)
header += '# Chromosome\t'
header += '\t'.join([
'Ratio', 'Sum <= {}'.format(args.distance), 'Sum > {}'.format(
args.distance)
] * len(args.matrices))
header += '\n'
file.write(header)
counter = 0
for i, chromosome in enumerate(chromosomes_list):
file.write('{}\t'.format(chromosome))
for j, matrix in enumerate(args.matrices):
if i < len(short_v_long_range[j]):
file.write('{}\t{}\t{}\t'.format(short_v_long_range[j][i],
sum_smaller[j][i],
sum_greater[j][i]))
else:
file.write('\t')
file.write('\n')
def main(args=None):
args = parse_arguments().parse_args(args)
for matrix in args.matrices:
# if
generated_by = None
genome_assembly = None
statistics = None
generated_by_cooler_lib = None
tool_url = None
matrix_generated_by = None
matrix_generated_by_url = None
creation_date = None
bin_length = None
size = None
nchroms = None
num_non_zero = None
min_non_zero = None
max_non_zero = None
sum_elements = None
num_nan_bins = None
if check_cooler(matrix) and args.no_metadata:
cooler_file = cooler.Cooler(matrix)
if cooler_file.info is not None:
# log.debug('cooler_file.info {}'.format(cooler_file.info))
if 'bin-size' in cooler_file.info:
bin_length = cooler_file.info['bin-size']
if 'nbins' in cooler_file.info:
size = cooler_file.info['nbins']
if 'nchroms' in cooler_file.info:
nchroms = cooler_file.info['nchroms']
# if 'chromosomes' in cooler_file.info:
# chromosomes = cooler_file.info['chromosomes']
if 'nnz' in cooler_file.info:
num_non_zero = cooler_file.info['nnz']
if 'min-value' in cooler_file.info:
min_non_zero = cooler_file.info['min-value']
if 'max-value' in cooler_file.info:
max_non_zero = cooler_file.info['max-value']
if 'generated-by' in cooler_file.info:
generated_by = toString(cooler_file.info['generated-by'])
if 'genome-assembly' in cooler_file.info:
genome_assembly = toString(
cooler_file.info['genome-assembly'])
if 'metadata' in cooler_file.info:
if cooler_file.info['metadata'] is not None:
if 'statistics' in cooler_file.info['metadata']:
statistics = cooler_file.info['metadata']['statistics']
if 'generated-by-cooler-lib' in cooler_file.info:
generated_by_cooler_lib = toString(
cooler_file.info['generated-by-cooler-lib'])
if 'tool-url' in cooler_file.info:
tool_url = toString(cooler_file.info['tool-url'])
if 'matrix-generated-by' in cooler_file.info:
matrix_generated_by = toString(
cooler_file.info['matrix-generated-by'])
if 'matrix-generated-by-url' in cooler_file.info:
matrix_generated_by_url = toString(
cooler_file.info['matrix-generated-by-url'])
if 'creation-date' in cooler_file.info:
creation_date = cooler_file.info['creation-date']
if 'sum-elements' in cooler_file.info:
sum_elements = cooler_file.info['sum-elements']
chromosome_sizes = cooler_file.chromsizes
else:
hic_ma = hm.hiCMatrix(matrix)
size = hic_ma.matrix.shape[0]
num_non_zero = hic_ma.matrix.nnz
sum_elements = ((hic_ma.matrix.sum() - hic_ma.matrix.diagonal().sum()) / 2) + hic_ma.matrix.diagonal().sum()
bin_length = hic_ma.getBinSize()
num_nan_bins = len(hic_ma.nan_bins)
min_non_zero = hic_ma.matrix.data.min()
max_non_zero = hic_ma.matrix.data.max()
# chromosomes = list(hic_ma.chrBinBoundaries)
chromosome_sizes = hic_ma.get_chromosome_sizes()
information = StringIO()
information.write(
"# Matrix information file. Created with HiCExplorer's hicInfo version {}\n".format(__version__))
if matrix is not None:
information.write("File:\t{}\n".format(matrix))
if creation_date is not None:
information.write("Date:\t{}\n".format(creation_date))
if genome_assembly is not None:
information.write("Genome assembly:\t{}\n".format(genome_assembly))
if size is not None:
information.write("Size:\t{:,}\n".format(size))
if bin_length is not None:
information.write("Bin_length:\t{}\n".format(bin_length))
if sum_elements is not None:
information.write("Sum of matrix:\t{}\n".format(sum_elements))
# if chromosomes is not None:
# information.write("Chromosomes:\t{}\n".format(
# ", ".join(toString(chromosomes))))
information.write("Chromosomes:length: ")
for key, value in chromosome_sizes.items():
information.write("{}: {} bp; ".format(key, value))
information.write('\n')
if nchroms is not None:
information.write("Number of chromosomes:\t{}\n".format(nchroms))
if num_non_zero is not None:
information.write(
"Non-zero elements:\t{:,}\n".format(num_non_zero))
if min_non_zero is not None:
information.write("Minimum (non zero):\t{}\n".format(min_non_zero))
if max_non_zero is not None:
information.write("Maximum:\t{}\n".format(max_non_zero))
if num_nan_bins is not None:
information.write("NaN bins:\t{}\n".format(num_nan_bins))
if check_cooler(matrix):
information.write('The following columns are available: {}\n'.format(
cooler.Cooler(matrix).bins().columns.values))
if generated_by is not None:
information.write("\n\nGenerated by:\t{}\n".format(generated_by))
if generated_by_cooler_lib is not None:
information.write("Cooler library version:\t{}\n".format(
generated_by_cooler_lib))
if tool_url is not None:
information.write("HiCMatrix url:\t{}\n".format(tool_url))
if matrix_generated_by is not None:
information.write(
"Interaction matrix created with:\t{}\n".format(matrix_generated_by))
if matrix_generated_by_url is not None:
information.write("URL:\t{}\n".format(matrix_generated_by_url))
if statistics is not None:
information.write("\n\nBuild statistics:\n{}\n".format(statistics))
if args.outFileName:
with open(args.outFileName, 'w') as file:
file.write(information.getvalue())
else:
print(information.getvalue())
information.close()
def adjustMatrix(pArgs):
if pArgs.chromosomes is not None and pArgs.regions is not None:
log.error('Please specify either --chromosomes or --regions.')
exit(1)
hic_matrix = None
if pArgs.chromosomes:
if check_cooler(pArgs.matrix) and len(pArgs.chromosomes) == 1 and pArgs.action == 'keep':
chromosomes_list = cooler.Cooler(pArgs.matrix).chromnames
if pArgs.chromosomes[0] in chromosomes_list:
hic_matrix = hm.hiCMatrix(pArgs.matrix, pChrnameList=pArgs.chromosomes)
else:
log.error('Chromosome not available in matrix: {} {}'.format(pArgs.matrix, pArgs.chromosomes[0]))
exit(1)
else:
hic_matrix = hm.hiCMatrix(pArgs.matrix)
chromosomes_list = list(hic_matrix.chrBinBoundaries)
chromosomes_list_to_operate_on = []
for chromosome in pArgs.chromosomes:
if chromosome in chromosomes_list:
chromosomes_list_to_operate_on.append(chromosome)
else:
log.warning('Chromosome not available in matrix: {} {}'.format(pArgs.matrix, chromosome))
if len(chromosomes_list_to_operate_on) == 0:
log.error('No valid chromosome given: {}. Available: {}'.format(pArgs.chromosomes, chromosomes_list))
exit(1)
if pArgs.action == 'keep':
hic_matrix.reorderChromosomes(chromosomes_list_to_operate_on)
elif pArgs.action == 'remove':
# chromosomes = list(hic_matrix.chrBinBoundaries)
for chromosome in chromosomes_list:
if chromosome in chromosomes_list_to_operate_on:
chromosomes_list.remove(chromosome)
hic_matrix.reorderChromosomes(chromosomes_list)
elif pArgs.action == 'mask':
hic_matrix.maskChromosomes(chromosomes_list_to_operate_on)
elif pArgs.regions:
hic_matrix = hm.hiCMatrix(pArgs.matrix)
chromosomes_list = list(hic_matrix.chrBinBoundaries)
genomic_regions = []
with open(pArgs.regions, 'r') as file:
for line in file.readlines():
_line = line.strip().split('\t')
if len(line) < 3:
log.warning("An entry shorter than 3 columns has been found!")
continue
if len(_line) >= 3:
chrom, start, end = _line[0], int(_line[1]), int(_line[2])
if chrom in chromosomes_list:
genomic_regions.append((chrom, start, end))
else:
log.warning('Chromosome not available in matrix, ignoring regions: {} {}'.format(pArgs.matrix, chrom))
if len(genomic_regions) == 0:
log.error('No valid chromosome given. Available: {}'.format(chromosomes_list))
exit(1)
# log.debug('genomic_regions {}'.format(genomic_regions))
matrix_indices_regions = []
for region in genomic_regions:
_regionBinRange = hic_matrix.getRegionBinRange(region[0], region[1], region[2])
if _regionBinRange is not None:
start, end = _regionBinRange
matrix_indices_regions.extend(list(range(start, end)))
# log.debug('matrix_indices_regions {}'.format(matrix_indices_regions))
if pArgs.action == 'keep':
values_submatrix = matrix_indices_regions
instances, features = hic_matrix.matrix.nonzero()
mask = np.isin(instances, values_submatrix)
mask = np.logical_not(mask)
hic_matrix.matrix.data[mask] = 0
hic_matrix.matrix.eliminate_zeros()
elif pArgs.action == 'mask':
hic_matrix.maskBins(matrix_indices_regions)
elif pArgs.action == 'remove':
full_matrix_range = np.array(range(0, max(hic_matrix.matrix.shape[0], hic_matrix.matrix.shape[1])))
matrix_indices_regions = np.array(matrix_indices_regions)
full_matrix_range[matrix_indices_regions] = -1
mask = full_matrix_range != -1
full_matrix_range = full_matrix_range[mask]
hic_matrix.reorderBins(full_matrix_range)
elif pArgs.maskBadRegions:
if check_cooler(pArgs.matrix) and len(pArgs.chromosomes) == 1 and pArgs.action == 'keep':
hic_matrix = hm.hiCMatrix(pArgs.matrix, pChrnameList=pArgs.chromosomes)
else:
hic_matrix = hm.hiCMatrix(pArgs.matrix)
else:
log.info('No data to adjust given. Please specify either --chromosomes or --region parameter.')
return hic_matrix
