def fetch_array(self, genome_range, genome_range2=None, balance=None, resolution='auto'):
"""
Parameters
----------
genome_range : {str, GenomeRange}
Intervals within input chromosome range.
genome_range2 : {str, GenomeRange}, optional.
balance : bool, optional
balance matrix or not,
default `self.is_balance`.
resolution : {'auto', int}
resolution of the data. for example 5000.
'auto' for calculate resolution automatically.
default 'auto'
Return
------
arr : numpy.ndarray
"""
from coolbox.utilities.hic.wrap import CoolerWrap
path = self.properties['file']
if balance is None:
balance = self.is_balance
wrap = CoolerWrap(path, balance=balance, binsize=resolution)
arr = wrap.fetch(genome_range, genome_range2)
return arr
def fetch_data(self, gr: GenomeRange, gr2=None, **kwargs) -> np.ndarray:
from coolbox.utilities.hic.wrap import CoolerWrap
path = self.properties['file']
binsize = kwargs.get('resolution',
self.properties.get('resolution', 'auto'))
wrap = CoolerWrap(path, balance=self.balance, binsize=binsize)
arr = wrap.fetch(gr, gr2)
self.fetched_binsize = wrap.fetched_binsize # expose fetched binsize
return self.fill_zero_nan(arr)
def fetch_matrix(self,
genome_range,
genome_range2=None,
resolution='auto') -> np.ndarray:
"""
${fetch_matrix}
"""
from coolbox.utilities.hic.wrap import CoolerWrap
path = self.properties['file']
wrap = CoolerWrap(path, balance=self.balance, binsize=resolution)
arr = wrap.fetch(genome_range, genome_range2)
self.fetched_binsize = wrap.fetched_binsize # expose fetched binsize
return self.fill_zero_nan(arr)