interval module

class mavis.interval.Interval(start, end=None, freq=1, number_type=None)

Bases: object

Parameters:

• start (int) – the start of the interval (inclusive)
• end (int) – the end of the interval (inclusive)
• freq (int) – the frequency or weight of the interval

__and__(other)

the intersection of two intervals

Example

>>> Interval(1, 10) & Interval(5, 50)
Interval(5, 10)
>>> Interval(1, 2) & Interval(10, 11)
None

__len__()

the length of the interval

Example

>>> len(Interval(1, 11))
12

Warning

only works for integer intervals

__or__(other)

the union of two intervals

Example

>>> Interval(1, 10) | Interval(5, 50)
Interval(1, 50)
>>> Interval(1, 2) | Interval(10, 11)
Interval(1, 11)

__sub__(other)

the difference of two intervals

Example

>>> Interval(1, 10) - Interval(5, 50)
[Interval(1, 4)]
>>> Interval(1, 2) - Interval(10, 11)
[Interval(1, 2)]
>>> Interval(1, 2) - Interval(-1, 10)
[]

__xor__(other)

center

the middle of the interval

Example

>>> Interval(1, 10).center
5.5
>>> Interval(1, 11).center
6

classmethod convert_pos(mapping, pos, forward_to_reverse=None)

classmethod convert_ratioed_pos(mapping, pos, forward_to_reverse=None)

convert any given position given a mapping of intervals to another range

Parameters:

• mapping (dict of Interval and Interval) – a mapping of a set of continuous intervals
• pos (int) – a position in the first coordinate system

Returns:

the position in the alternate coordinate system given the input mapping

Return type:

int

Raises:

• AttributeError – if the input position is outside the set of input segments
• IndexError – if the input position cannot be converted to the output system

Example

>>> mapping = {(1, 10): (101, 110), (11, 20): (555, 564)}
>>> Interval.convert_pos(mapping, 5)
5
>>> Interval.convert_pos(mapping, 15)
559

classmethod dist(first, other)

returns the minimum distance between intervals

Example

>>> Interval.dist((1, 4), (5, 7))
-1
>>> Interval.dist((5, 7), (1, 4))
1
>>> Interval.dist((5, 8), (7, 9))
0

classmethod intersection(*intervals)

returns None if there is no intersection

Example

>>> Interval.intersection((1, 10), (2, 8), (7, 15))
Interval(7, 8)
>>> Interval.intersection((1, 2), (5, 9))
None

length()

classmethod min_nonoverlapping(*intervals)

for a list of intervals, orders them and merges any overlap to return a list of non-overlapping intervals O(nlogn)

Example

>>> Interval.min_nonoverlapping((1, 10), (7, 8), (6, 14), (17, 20))
[Interval(1, 14), Interval(17, 20)]

classmethod overlaps(first, other)

checks if two intervals have any portion of their given ranges in common

Parameters:

• first (Interval) – an interval to be compared
• other (Interval) – an interval to be compared

Example

>>> Interval.overlaps(Interval(1, 4), Interval(5, 7))
False
>>> Interval.overlaps(Interval(1, 10), Interval(10, 11))
True
>>> Interval.overlaps((1, 10), (10, 11))
True

classmethod position_in_range(segments, pos)

classmethod split_overlap(*intervals, weight_mapping={})

for a given set of intervals splits any overlap so that the result is a new list of intervals with a single bp overlap

Warning

this method is meant for integer intervals only

classmethod union(*intervals)

returns the union of the set of input intervals

Example

>>> Interval.union((1, 2), (4, 6), (4, 9), (20, 21))
Interval(1, 21)

class mavis.interval.IntervalMapping(mapping=None, opposing=None)

Bases: object

mapping between coordinate systems using intervals. source intervals cannot overlap but no such assertion is enforced on the target intervals

add(src_interval, tgt_interval, opposing_directions=True)

convert_pos(pos, simplify=True)

convert any given position given a mapping of intervals to another range

Parameters:pos (int) – a position in the first coordinate system Returns:the position in the alternate coordinate system given the input mapping - int: if simplify is True - Interval: if simplify is False Raises:IndexError – if the input position is not in any of the mapped intervals

Example

>>> mapping = IntervalMapping(mapping={(1, 10): (101, 110), (11, 20): (555, 564)})
>>> mapping.convert_pos(5)
5
>>> mapping.convert_pos(15)
559