def read_as_intervaltree(self):
'''
Reads the data from a 'bed' file into an ``intervaltree_bio.GenomeIntervalTree`` data structure.
Similarly to ``open`` and ``open_text`` it won't download file to cache, if it is not there.
Reads the whole file to memory during its work.
The file must be a `bed` or `bed.gz` file.
The ``data`` field of each interval will contain the result of ``ln.split('\t')[3:]`` applied to the corresponding line of the ``bed`` file.
Returns:
a GenomeIntervalTree instance.
'''
assert self['type'] in ['bed', 'narrowPeak', 'broadPeak']
with self.open_text() as f:
gtree = GenomeIntervalTree.from_bed(fileobj=f)
return gtree
def read_as_intervaltree(self):
'''
Reads the data from a 'bed' file into an ``intervaltree_bio.GenomeIntervalTree`` data structure.
Similarly to ``open`` and ``open_text`` it won't download file to cache, if it is not there.
Reads the whole file to memory during its work.
The file must be a `bed` or `bed.gz` file.
The ``data`` field of each interval will contain the result of ``ln.split('\t')[3:]`` applied to the corresponding line of the ``bed`` file.
Returns:
a GenomeIntervalTree instance.
'''
assert self['type'] in ['bed', 'narrowPeak', 'broadPeak']
with self.open_text() as f:
gtree = GenomeIntervalTree.from_bed(fileobj=f)
return gtree
def bed_to_tree(bed):
with open(bed, 'r') as f:
btree = GenomeIntervalTree.from_bed(fileobj=f)
return btree