intervalframe.IntervalFrame

class intervalframe.IntervalFrame(intervals=None, df=None, labels=None, columns=None, dtypes=None, copy_df=False, copy_intervals=False)

Annotated augmented interval list

IntervalFrame stores a intervals

Attributes

columns
iloc
loc
shape
values

Methods

annotate(iframe, column[, method, column_name])	Annotate values in one IntervalFrame with another
bin_coverage([bin_size, min_length, max_length])	Find sum of coverage within binned positions
bin_nhits([bin_size, min_length, max_length])	Find number of intervals overlapping binned positions
combine(iframe_list[, combine_method, ...])	Combine two IntervalFrames
concat(iframe_iter)	Append IntervalFrame to current IntervalFrame
copy()	Copy IntervalFrame
coverage()	Find number of intervals overlapping every position in the IntervalFrame
difference(iframe)	Remove any overlapping intervals
downsample(proportion)	Randomly downsample intervals
drop_columns(columns)	Drop columns from IntervalFrame
ends()
exact_match(iframe)	Find exact matches between LabeledIntervalArrays
from_array(starts, ends[, labels])
from_dict_range(dict_range[, bin_size])
intersect(start, end[, label])	Find intersecting intervals
iter_intersect(iframe)
length_dist()	Calculate length distribution of intervals
merge([gap])	Annotate values in one IntervalFrame with another
nhits(start, end[, label])	Find number of intersecting intervals
overlap(iframe[, key])	Find overlaps in one IntervalFrame with another
read_bed(filename[, header, skipfirst, is_url])	Read BED file into IntervalFrame
read_h5(h5_group)	Read IntervalFrame to h5py group
read_parquet(filename)	Read parquet file into IntervalFrame
segment(column[, method, cutoff, hazard, ...])	Annotate values in one IntervalFrame with another
sparse_optimize([fill_value])	Optimize for sparse IntervalFrames
starts()
subtract(iframe)	Subtract intersecting regions for IntervalFrame
to_h5(h5_group[, compression_opts])	Write IntervalFrame to h5py group
to_parquet(filename, **kwargs)	Write IntervalFrame to parquet file
wps([protection, min_length, max_length])	Calculate Window Protection Score for each position in AIList range