def fetch_pixels(self,
genome_range,
genome_range2=None,
balance=None,
resolution='auto',
join=True):
"""
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'
join : bool
whether to expand the bin ID columns
into (chrom, start, end).
default True
Return
------
pixels : pandas.core.frame.DataFrame
Hi-C pixels table.
The pixel table contains the non-zero upper triangle entries of the contact map.
"""
from coolbox.utilities.hic.wrap import CoolerWrap
genome_range = to_gr(genome_range)
if genome_range2 is not None:
genome_range2 = to_gr(genome_range2)
path = self.properties['file']
if balance is None:
balance = self.is_balance
wrap = CoolerWrap(path, balance=balance, binsize=resolution)
pixels = wrap.fetch_pixels(genome_range, genome_range2, join=join)
return pixels
def fetch_pixels(self, gr: GenomeRange, **kwargs):
"""
Fetch the pixels table of upper triangle of the original contact matrix(not processed).
Parameters
----------
gr2 : 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'
join : bool
whether to expand the bin ID columns
into (chrom, start, end).
default True
Returns
-------
pixels : pandas.core.frame.DataFrame
Hi-C pixels table.
The pixel table contains the non-zero upper triangle entries of the contact map.
"""
from coolbox.utilities.hic.wrap import CoolerWrap
path = self.properties['file']
balance = kwargs.get('balance', self.is_balance)
wrap = CoolerWrap(path,
balance=balance,
binsize=kwargs.get('resolution', 'auto'))
pixels = wrap.fetch_pixels(gr,
kwargs.get('gr2'),
join=kwargs.get('join', True))
return pixels