def getRegion(args, ma):
chrom = region_start = region_end = idx1 = start_pos1 = chrom2 = region_start2 = region_end2 = idx2 = start_pos2 = None
chrom, region_start, region_end = translate_region(args.region)
chrom = check_chrom_str_bytes(ma.interval_trees, chrom)
# if type(next(iter(ma.interval_trees))) in [np.bytes_, bytes]:
# chrom = toBytes(chrom)
if chrom not in list(ma.interval_trees):
chrom = change_chrom_names(chrom)
chrom = check_chrom_str_bytes(ma.interval_trees, chrom)
# if type(next(iter(ma.interval_trees))) in [np.bytes_, bytes]:
# chrom = toBytes(chrom)
if chrom not in list(ma.interval_trees):
exit("Chromosome name {} in --region not in matrix".format(change_chrom_names(chrom)))
args.region = [chrom, region_start, region_end]
is_cooler = check_cooler(args.matrix)
if is_cooler:
idx1, start_pos1 = zip(*[(idx, x[1]) for idx, x in enumerate(ma.cut_intervals) if x[0] == chrom and
((x[1] >= region_start and x[2] < region_end) or
(x[1] < region_end and x[2] < region_end and x[2] > region_start) or
(x[1] > region_start and x[1] < region_end))])
else:
idx1, start_pos1 = zip(*[(idx, x[1]) for idx, x in enumerate(ma.cut_intervals) if x[0] == chrom and
x[1] >= region_start and x[2] < region_end])
if args.region2:
chrom2, region_start2, region_end2 = translate_region(args.region2)
chrom2 = check_chrom_str_bytes(ma.interval_trees, chrom2)
# if type(next(iter(ma.interval_trees))) in [np.bytes_, bytes]:
# chrom2 = toBytes(chrom)
if chrom2 not in list(ma.interval_trees):
chrom2 = change_chrom_names(chrom2)
chrom2 = check_chrom_str_bytes(ma.interval_trees, chrom2)
# if type(next(iter(ma.interval_trees))) in [np.bytes_, bytes]:
# chrom2 = toBytes(chrom)
if chrom2 not in list(ma.interval_trees):
exit("Chromosome name {} in --region2 not in matrix".format(change_chrom_names(chrom2)))
if is_cooler:
idx2, start_pos2 = zip(*[(idx, x[1]) for idx, x in enumerate(ma.cut_intervals) if x[0] == chrom2 and
((x[1] >= region_start2 and x[2] < region_end2) or
(x[1] < region_end2 and x[2] < region_end2 and x[2] > region_start2) or
(x[1] > region_start2 and x[1] < region_end2))])
else:
idx2, start_pos2 = zip(*[(idx, x[1]) for idx, x in enumerate(ma.cut_intervals) if x[0] == chrom2 and
x[1] >= region_start2 and x[2] < region_end2])
else:
idx2 = idx1
chrom2 = chrom
start_pos2 = start_pos1
return chrom, region_start, region_end, idx1, start_pos1, chrom2, region_start2, region_end2, idx2, start_pos2
def translate_region(region_string, ma):
"""
Takes an string and returns a list
of chrom, start, end.
If the region string only contains
the chrom, then start and end
are set to matrix start and end on this chromosome
"""
# region_string = toBytes(region_string)
region_string = region_string.replace(",", "")
region_string = region_string.replace(";", "")
region_string = region_string.replace("!", "")
region_string = region_string.replace("-", ":")
fields = region_string.split(":")
chrom = fields[0]
chrom = check_chrom_str_bytes(ma.interval_trees, chrom)
if chrom not in list(ma.interval_trees):
chrom = change_chrom_names(chrom)
chrom = check_chrom_str_bytes(ma.interval_trees, chrom)
if chrom not in list(ma.interval_trees):
exit(
"Chromosome name {} in --region not in matrix".format(change_chrom_names(chrom)))
first_bin, last_bin = ma.getChrBinRange(chrom)
try:
region_start = int(fields[1])
except IndexError:
region_start = ma.getBinPos(first_bin)[1]
try:
region_end = int(fields[2])
except IndexError:
region_end = ma.getBinPos(last_bin - 1)[2]
return chrom, region_start, region_end
def plotBigwig(pAxis, pNameOfBigwigList, pChromosomeSizes=None, pRegion=None, pXticks=None, pFlipBigwigSign=None, pScaleFactorBigwig=None,
pValueMin=None, pValueMax=None):
log.debug('plotting eigenvector')
pAxis.set_frame_on(False)
pAxis.xaxis.set_visible(False)
# pNameOfBigwigList is not a list, but to make room for future options
# requiring more than one bigwig file I set this to a list intentionally.
pNameOfBigwigList = [pNameOfBigwigList]
file_format = pNameOfBigwigList[0].split(".")[-1]
if file_format != 'bigwig' and file_format != 'bw':
log.error("Given files are not bigwig")
exit()
for bigwig_file in pNameOfBigwigList:
if bigwig_file.split('.')[-1] != file_format:
log.error("Eigenvector input files have different formats.")
exit()
x_values = []
bigwig_scores = []
if file_format == "bigwig" or file_format == 'bw':
for i, bigwigFile in enumerate(pNameOfBigwigList):
bw = pyBigWig.open(bigwigFile)
bigwig_scores = []
if pRegion:
chrom, region_start, region_end = pRegion
# region_end could be a very large number returned by translate_region
region_end = min(region_end, pChromosomeSizes[chrom])
# log.info("chromosomes bigwig: {}".format(bw.chroms()))
chrom = check_chrom_str_bytes(bw.chroms(), chrom)
if chrom not in list(bw.chroms().keys()):
chrom = change_chrom_names(chrom)
if chrom not in list(bw.chroms().keys()):
log.info("bigwig file has no chromosome named: {}.".format(chrom))
return
# the bigwig file may end before the region end, to avoid and error
# the bigwig_end is set for the pyBigwig query
bigwig_end = min(bw.chroms()[chrom], region_end)
# TODO, this could be a parameters
num_bins = min(1000, int(bigwig_end - region_start) / 10)
scores_per_bin = np.array(bw.stats(chrom, region_start, bigwig_end, nBins=num_bins)).astype(float)
if scores_per_bin is None:
log.info("Chromosome {} has no entries in bigwig file.".format(chrom))
return
_x_vals = np.linspace(region_start, region_end, num_bins)
assert len(_x_vals) == len(scores_per_bin)
x_values.extend(_x_vals)
bigwig_scores.extend(scores_per_bin)
pAxis.set_xlim(region_start, region_end)
elif pChromosomeSizes:
chrom_length_sum = 0
for chrom in pChromosomeSizes:
chrom_ = check_chrom_str_bytes(bw.chroms(), chrom)
if chrom_ not in list(bw.chroms().keys()):
log.info("bigwig file as no chromosome named: {}.".format(chrom))
return
# chrom = check_chrom_str_bytes(pChromosomeSizes, chrom)
# set the bin size to approximately 100kb
# or to the chromosome size if this happens to be less than 100kb
chunk_size = min(1e5, pChromosomeSizes[chrom])
num_bins = int(pChromosomeSizes[chrom] / chunk_size)
scores_per_bin = np.array(bw.stats(chrom_, 0, pChromosomeSizes[chrom], nBins=num_bins)).astype(float)
if scores_per_bin is None:
log.info("Chromosome {} has no entries in bigwig file.".format(chrom))
return
_x_vals = np.linspace(chrom_length_sum, chrom_length_sum + pChromosomeSizes[chrom], num_bins)
assert len(_x_vals) == len(scores_per_bin)
x_values.extend(_x_vals)
bigwig_scores.extend(scores_per_bin)
chrom_length_sum += pChromosomeSizes[chrom]
pAxis.set_xlim(0, chrom_length_sum)
log.debug("Number of data points: {}".format(len(bigwig_scores)))
if pFlipBigwigSign:
log.info("Flipping sign of bigwig values.")
bigwig_scores = np.array(bigwig_scores)
bigwig_scores *= -1
if pScaleFactorBigwig is not None and pScaleFactorBigwig != 1.0:
log.info("Scaling bigwig values.")
bigwig_scores = np.array(bigwig_scores)
bigwig_scores *= pScaleFactorBigwig
if pValueMin is not None or pValueMax is not None
bigwig_scores = bigwig_scores.clip(pValueMin, pValueMax)
# else:
# for i, bigwigFile in enumerate(pNameOfBigwigList):
# interval_tree, min_value, max_value = file_to_intervaltree(bigwigFile)
# eigenvector = []
# if pChromosomeSizes:
# for chrom in pChromosomeSizes:
# if toString(chrom) not in interval_tree:
# log.info("Chromosome with no entry in the eigenvector found. Please exclude it from the matrix: {}. The eigenvector is left empty.".format(chrom))
# return
# for i, region in enumerate(sorted(interval_tree[toString(chrom)])):
# if i == 0:
# region_start = region[0]
# region_end = region[1]
# eigenvector.append(complex(region.data[0]).real)
# x = np.arange(0, len(eigenvector), 1)
# pAxis.set_xlim(0, len(eigenvector))
#
# elif pRegion:
# if toString(chrom) not in interval_tree:
# log.info("Chromosome with no entry in the eigenvector found. Please exclude it from the matrix: {}. The eigenvector is left empty.".format(chrom))
# return
# for region in sorted(interval_tree[toString(chrom)][region_start:region_end]):
# eigenvector.append(float(region.data[0]))
# step = (region_end * 2 - region_start) // len(eigenvector)
#
# x = np.arange(region_start, region_end * 2, int(step))
# while len(x) < len(eigenvector):
# x = np.append(x[-1] + int(step))
# while len(eigenvector) < len(x):
# x = x[:-1]
#
# pAxis.set_xlim(region_start, region_end * 2)
if x_values is not None and bigwig_scores is not None:
pAxis.fill_between(x_values, 0, bigwig_scores, edgecolor='none')
def plotBigwig(pAxis, pNameOfBigwigList, pChromosomeSizes=None, pRegion=None, pXticks=None, pFlipBigwigSign=None, pScaleFactorBigwig=None, pVertical=False,
pValueMin=None, pValueMax=None):
log.debug('plotting eigenvector')
# pNameOfBigwigList is not a list, but to make room for future options
# requiring more than one bigwig file I set this to a list intentionally.
# pNameOfBigwigList = [pNameOfBigwigList]
for file in pNameOfBigwigList:
file_format = file.split(".")[-1]
if file_format != 'bigwig' and file_format != 'bw':
log.error("Given files are not bigwig")
exit(1)
# for bigwig_file in pNameOfBigwigList:
# if bigwig_file.split('.')[-1] != file_format:
# log.error("Eigenvector input files have different formats.")
# exit()
if file_format == "bigwig" or file_format == 'bw':
for i, bigwigFile in enumerate(pNameOfBigwigList):
x_values = []
bigwig_scores = []
pAxis[i].set_frame_on(False)
if pVertical:
pAxis[i].yaxis.set_visible(False)
else:
# pAxis[i].set_frame_on(False)
pAxis[i].xaxis.set_visible(False)
bw = pyBigWig.open(bigwigFile)
bigwig_scores = []
if pRegion:
chrom, region_start, region_end = pRegion
# region_end could be a very large number returned by translate_region
region_end = min(region_end, pChromosomeSizes[chrom])
# log.info("chromosomes bigwig: {}".format(bw.chroms()))
chrom = check_chrom_str_bytes(bw.chroms(), chrom)
if chrom not in list(bw.chroms().keys()):
chrom = change_chrom_names(chrom)
if chrom not in list(bw.chroms().keys()):
log.info("bigwig file has no chromosome named: {}.".format(chrom))
return
# the bigwig file may end before the region end, to avoid and error
# the bigwig_end is set for the pyBigwig query
bigwig_end = min(bw.chroms()[chrom], region_end)
# TODO, this could be a parameters
num_bins = min(1000, int(bigwig_end - region_start) / 10)
scores_per_bin = np.array(bw.stats(chrom, region_start, bigwig_end, nBins=num_bins)).astype(float)
if scores_per_bin is None:
log.info("Chromosome {} has no entries in bigwig file.".format(chrom))
return
_x_vals = np.linspace(region_start, region_end, num_bins)
assert len(_x_vals) == len(scores_per_bin)
x_values.extend(_x_vals)
bigwig_scores.extend(scores_per_bin)
if pVertical:
pAxis[i].set_ylim(region_start, region_end)
else:
pAxis[i].set_xlim(region_start, region_end)
elif pChromosomeSizes:
chrom_length_sum = 0
for chrom in pChromosomeSizes:
chrom_ = check_chrom_str_bytes(bw.chroms(), chrom)
if chrom_ not in list(bw.chroms().keys()):
log.info("bigwig file as no chromosome named: {}.".format(chrom))
return
# chrom = check_chrom_str_bytes(pChromosomeSizes, chrom)
# set the bin size to approximately 100kb
# or to the chromosome size if this happens to be less than 100kb
chunk_size = min(1e5, pChromosomeSizes[chrom])
num_bins = int(pChromosomeSizes[chrom] / chunk_size)
scores_per_bin = np.array(bw.stats(chrom_, 0, pChromosomeSizes[chrom], nBins=num_bins)).astype(float)
if scores_per_bin is None:
log.info("Chromosome {} has no entries in bigwig file.".format(chrom))
return
_x_vals = np.linspace(chrom_length_sum, chrom_length_sum + pChromosomeSizes[chrom], num_bins)
assert len(_x_vals) == len(scores_per_bin)
x_values.extend(_x_vals)
bigwig_scores.extend(scores_per_bin)
chrom_length_sum += pChromosomeSizes[chrom]
if pVertical:
pAxis[i].set_ylim(0, chrom_length_sum)
else:
pAxis[i].set_xlim(0, chrom_length_sum)
log.debug("Number of data points: {}".format(len(bigwig_scores)))
bigwig_scores = np.array(bigwig_scores)
if pFlipBigwigSign:
log.info("Flipping sign of bigwig values.")
bigwig_scores *= -1
if pScaleFactorBigwig is not None and pScaleFactorBigwig != 1.0:
log.info("Scaling bigwig values.")
bigwig_scores *= pScaleFactorBigwig
if pValueMin is not None or pValueMax is not None:
bigwig_scores = bigwig_scores.clip(pValueMin, pValueMax)
if x_values is not None and bigwig_scores is not None:
if pVertical:
pAxis[i].fill_between(np.flip(bigwig_scores, 0), x_values, edgecolor='none')
else:
pAxis[i].fill_between(x_values, 0, bigwig_scores, edgecolor='none')