ailist.AIList

class ailist.AIList

Wrapper for C ailist_t

AIList stores a list of intervals

Attributes

first	Start of first interval in AIList
idxC	Index of components in constructed AIList
is_closed	'bool'
is_constructed	'bool'
is_frozen	'bool'
last	End of last intervals in AIList
lenC	Length of components in constructed AIList
nc	Number of components in constructed AIList
range	AIList.last - AIList.first
size	Number of intervals in AIList

Methods

add(self, int start, int end[, id_value])	Add an interval to AIList inplace
append(self, AIList query_ail)	Union of intervals within two AIList
bin_coverage(self, int bin_size=100000[, ...])	Find sum of coverage within binned positions
bin_nhits(self, int bin_size=100000[, ...])	Find number of intervals overlapping binned positions
close(self)	Close object and clear memory
common(self, AIList query_ail)	Common intervals within another AIList
construct(self, int min_length=20)	Construct ailist_t *Required to call intersect
copy(self)
coverage(self)	Find number of intervals overlapping every position in the AList range
display(self)	Print all intervals
downsample(self, double proportion)	Randomly downsample AIList
extract_ends(self)	Return the end values
extract_id(self)	Return the ID values
extract_starts(self)	Return the start values
filter(self, int min_length=1, ...)	Filter out intervals outside of a length range
freeze(self)	Make AIList immutable
from_array(self, const long[, const long[, ...)	Add intervals from arrays to AIList inplace
intersect(self, int start, int end)	Find intervals overlapping given range
intersect_from_ailist(self, AIList ail_query)	Find interval indices overlapping given ranges
intersect_from_array(self, const long[, ...)	Find interval indices overlapping given ranges
intersect_ids(self, int start, int end)	Find interval indices overlapping given range
interval_coverage(self, int start, int end)	Find number of intervals overlapping each position in given interval
iter_sorted(self)	Iterate over an AIList in sorted way
length_dist(self)	Calculate length distribution of intervals
merge(self, int gap=0)	Merge intervals within a gap
nhits(self, start, end[, min_length, max_length])	Find number of intervals overlapping binned positions
nhits_from_array(self, const long[, const long[)	Find number of intervals overlapping given positions
subtract(self, AIList query_ail)	Subtract intervals within another AIList
unfreeze(self)	Make AIList mutable
wps(self, int protection=60[, min_length, ...])	Calculate Window Protection Score for each position in AIList range