def fetch(self, genome_range1, genome_range2=None):
"""
Return
------
matrix : numpy.ndarray
"""
from coolbox.utilities.genome import GenomeRange
if genome_range2 is None:
genome_range2 = genome_range1
genome_range1 = to_gr(genome_range1)
genome_range2 = to_gr(genome_range2)
if isinstance(genome_range1, str):
genome_range1 = GenomeRange(genome_range1)
if isinstance(genome_range2, str):
genome_range2 = GenomeRange(genome_range2)
if genome_range1.chrom.startswith("chr"):
genome_range1.change_chrom_names()
if genome_range2.chrom.startswith("chr"):
genome_range2.change_chrom_names()
binsize = self.infer_binsize(genome_range1)
self.fetched_binsize = binsize # expose fetched binsize
straw_list = self.__fetch_straw_list(genome_range1, genome_range2, binsize)
matrix = self.__list_to_matrix(straw_list, genome_range1, genome_range2, binsize)
return matrix
def fetch(self, genome_range1, genome_range2=None):
# TODO what if genome_ranges are invalid
if genome_range2 is None:
genome_range2 = genome_range1
genome_range1 = to_gr(genome_range1)
genome_range2 = to_gr(genome_range2)
cool = self.get_cool(genome_range1)
if genome_range1.chrom not in cool.chromnames:
genome_range1.change_chrom_names()
if genome_range2.chrom not in cool.chromnames:
genome_range2.change_chrom_names()
try:
mat = cool.matrix(balance=self.balance).fetch(
str(genome_range1), str(genome_range2))
except ValueError as e:
log.warning(str(e))
log.warning(
"Data is not balanced, force to use unbalanced matrix.")
mat = cool.matrix(balance=False).fetch(str(genome_range1),
str(genome_range2))
return mat
def infer_binsize(self, genome_range):
from .tools import infer_resolution
genome_range = to_gr(genome_range)
if self.is_multi:
resolutions = [k for k in self.coolers.keys()]
if self.binsize == 'auto':
binsize = infer_resolution(genome_range, resolutions)
else:
assert self.binsize in resolutions, \
"Multi-Cooler file not contain the resolution {}.".format(self.binsize)
binsize = int(self.binsize)
else:
binsize = self.cool.binsize
return binsize
def fetch(self, gr1, gr2=None):
"""
Return
------
matrix : numpy.ndarray
"""
from coolbox.utilities.genome import GenomeRange
flip = False
if gr2 is None:
gr2 = gr1
gr1 = to_gr(gr1)
gr2 = to_gr(gr2)
if gr2.start < gr1.start:
flip = True
gr1, gr2 = gr2, gr1
if isinstance(gr1, str):
gr1 = GenomeRange(gr1)
if isinstance(gr2, str):
gr2 = GenomeRange(gr2)
if gr1.chrom.startswith("chr"):
gr1.change_chrom_names()
if gr2.chrom.startswith("chr"):
gr2.change_chrom_names()
binsize = self.infer_binsize(gr1)
self.fetched_binsize = binsize # expose fetched binsize
straw_iter = self.__fetch_straw_iter(gr1, gr2, binsize)
mat = self.__straw_to_matrix(straw_iter, gr1, gr2, binsize)
if flip:
mat = mat.T
return mat