ailist.LabeledIntervalArray

class ailist.LabeledIntervalArray

Wrapper for C labeled_aiarray_t

LabeledIntervalArray stores a list of intervals

Attributes

ends	End values
is_closed	'bool'
is_constructed	Whether LabeledIntervalArray is constructed or not
is_frozen	'bool'
label_counts	Count number of intervals per label
label_ranges	Ranges(start, end) for each label
labels	Label values
size	Number of intervals in LabeledIntervalArray
starts	Start values
unique_labels	Array of unique labels

Methods

add(self, start, end, label)	Add an interval to LabeledIntervalArray inplace
append(self, LabeledIntervalArray other_ail)	Add intervals from arrays to LabeledIntervalArray inplace
bin_nhits(self, int bin_size=100000[, ...])	Find number of intervals overlapping binned positions
close(self)	Close object and clear memory
common(self, LabeledIntervalArray other_laia)	Finds the common intervals between two LabeledIntervalArrays
construct(self, int min_length=20)	Construct labeled_aiarray_t *Required to call intersect
copy(self)	Copy LabeledIntervalArray
coverage(self[, labels, min_length, max_length])	Calculate coverage for each position in LabeledIntervalArray range
create_bin(dict_range[, bin_size])
downsample(self, double proportion[, ...])	Randomly downsample LabeledIntervalArray
filter(self, int min_length=1, ...)	Filter out intervals outside of a length range
filter_exact_match(self, ...)	Determine which intervals are present
freeze(self)	Make LabeledIntervalArray immutable
get(self, label[, return_intervals, ...])	Get LabeledIntervalArray for given label
get_ail(self, label)
get_locs(self, labels)
has_exact_match(self, ...)	Determine which intervals are present
has_hit(self, start, end, label)	Find interval indices overlapping given ranges
index_with_aiarray(self, ...)
intersect(self, start, end, label[, ...])	Find intervals overlapping given range
intersect_from_LabeledIntervalArray(self, ...)	Find interval indices overlapping given ranges
is_exact_match(self, ...)	Determine which intervals are present
iter_intersect(self, ...[, ...])
iter_sorted(self)	Iterate over an LabeledIntervalArray in sorted way
length_dist(self)	Calculate length distribution of intervals
merge(self, int gap=0)	Merge intervals within a gap
midpoint_coverage(self[, labels, ...])	Calculate coverage for each position in LabeledIntervalArray range
nhits(self, start, end, label[, min_length, ...])	Find number of intervals overlapping given positions
nhits_from_LabeledIntervalArray(self, ...[, ...])	Find number of intervals overlapping
percent_coverage(self, ...)	Finds the percent coverage of two LabeledIntervalArrays
set_ail(self, AIList ail, unicode label)
simulate(self)
sort(self)
sorted_index(self)
subtract(self, LabeledIntervalArray other_laia)	Finds the subtraction of two LabeledIntervalArrays
unfreeze(self)	Make LabeledIntervalArray mutable
union(self, LabeledIntervalArray other_laia)	Finds the union of two LabeledIntervalArrays
validate_construction(self)	Validates the construction of the LabeledIntervalArray
where_interval(self, start, end, label)	Determine which intervals are present
which_exact_match(self, ...)	Determine which intervals are present
wps(self, int protection=60[, labels, ...])	Calculate Window Protection Score for each position in LabeledIntervalArray range