ngs_tools.gtf.SegmentCollection

Module Contents

Classes

SegmentCollection

Class to represent a collection of integer interval segments, zero-indexed.

exception ngs_tools.gtf.SegmentCollection.SegmentCollectionError

Bases: Exception

Common base class for all non-exit exceptions.

class ngs_tools.gtf.SegmentCollection.SegmentCollection(segments: Optional[List[ngs_tools.gtf.Segment.Segment]] = None)

Class to represent a collection of integer interval segments, zero-indexed. The segments are always sorted and overlaps are collapsed.

_segments

List of Segment instances; for internal use only. Use segments instead.

property segments: List[ngs_tools.gtf.Segment.Segment]

Get a list of Segment instances

property start: int

Leftmost value of all segments. 0 if there are no segments.

property end: int

Rightmost value of all segments. 0 if there are no segments.

add_segment(segment: ngs_tools.gtf.Segment.Segment)

Add a segment to the collection.

Parameters:

segment – Segment to add

add_collection(collection: SegmentCollection)

Add a collection of segments to the collection.

Parameters:

collection – Collection to add

__iter__()

__getitem__(i)

__len__()

__bool__()

__eq__(other: SegmentCollection)

Return self==value.

invert(bounds: ngs_tools.gtf.Segment.Segment) → SegmentCollection

Invert this SegmentCollection within the given bounds.

Parameters:

bounds – The bounds to invert with respect to.

Returns:

A new SegmentCollection that is inverted

Raises:

SegmentCollectionError – If bounds does not entirely contain this collection

collapse()

Collapse the segments in this collection such that there are no overlapping segments. Any overlapping segments are merged into a single large segment.

span_is_exclusive(collection: SegmentCollection) → bool

Evaluate whether the span of this collection is exclusive of that of another collection.

Parameters:

collection – SegmentCollection object to check

Returns:

True or False

is_overlapping(collection: SegmentCollection) → bool

Evaluate whether this collection overlaps with another collection.

Parameters:

collection – SegmentCollection object to check

Returns:

True or False

is_subset(collection: SegmentCollection) → bool

Evaluate whether this collection is a subset of another collection.

Parameters:

collection – SegmentCollection object to check

Returns:

True or False

is_superset(collection: SegmentCollection) → bool

Evaluate whether this collection is a superset of another collection.

Parameters:

collection – SegmentCollection object to check

Returns:

True or False

flank(l: int, left: Optional[int] = None, right: Optional[int] = None) → SegmentCollection

Construct a new segment collection where all the segments have start and end flanks of length l. Optionally, limit the span of the new segment collection. This is done by calling Segment.flank() on all the segments and initializing a new SegmentCollection. Any overlaps are collapsed.

Parameters:

• l – Flank length

• left – Clip the resulting collection’s start to this value. Defaults to None. If not provided, no clipping is performed.

• right – Clip the resulting collection’s end to this value. Defaults to None. If not provided, no clipping is performed.

Returns:

The new collection

classmethod from_positions(positions: Union[List[int], Set[int]]) → SegmentCollection

Initialize a new collection given a list or set of integer positions.

Parameters:

positions – Integer positions to construct the collection from

Returns:

The new collection

classmethod from_collections(*collections: SegmentCollection) → SegmentCollection

Initialize a new collection given an arbitrary number of collections.

Parameters:

*collections – The collections to combine

Returns:

The new collection

__repr__()

Return repr(self).