:py:mod:`pyranges.multioverlap`
===============================

.. py:module:: pyranges.multioverlap


Module Contents
---------------


Functions
~~~~~~~~~

.. autoapisummary::

   pyranges.multioverlap.count_overlaps



.. py:function:: count_overlaps(grs, features=None, strandedness=None, how=None, nb_cpu=1)

   Count overlaps in multiple pyranges.

   :param grs: The PyRanges to use as queries.
   :type grs: dict of PyRanges
   :param features: The PyRanges to use as subject in the query. If None, the PyRanges themselves are used as a query.
   :type features: PyRanges, default None
   :param strandedness:    Whether to compare PyRanges on the same strand, the opposite or ignore strand
                           information. The default, None, means use "same" if both PyRanges are stranded,
                           otherwise ignore the strand information.

                        how : {None, "all", "containment"}, default None, i.e. all

                           What intervals to report. By default reports all overlapping intervals. "containment"
                           reports intervals where the overlapping is contained within it.
   :type strandedness: {None, "same", "opposite", False}, default None, i.e. auto
   :param nb_cpu: How many cpus to use. Can at most use 1 per chromosome or chromosome/strand tuple.
                  Will only lead to speedups on large datasets.
   :type nb_cpu: int, default 1

   .. rubric:: Examples

   >>> a = '''Chromosome Start End
   ... chr1    6    12
   ... chr1    10    20
   ... chr1    22    27
   ... chr1    24    30'''

   >>> b = '''Chromosome Start End
   ... chr1    12    32
   ... chr1    14    30'''

   >>> c = '''Chromosome Start End
   ... chr1    8    15
   ... chr1    10    14
   ... chr1    32    34'''

   >>> grs = {n: pr.from_string(s) for n, s in zip(["a", "b", "c"], [a, b, c])}
   >>> for k, v in grs.items():
   ...     print("Name: " + k)
   ...     print(v)
   Name: a
   +--------------+-----------+-----------+
   | Chromosome   |     Start |       End |
   | (category)   |   (int64) |   (int64) |
   |--------------+-----------+-----------|
   | chr1         |         6 |        12 |
   | chr1         |        10 |        20 |
   | chr1         |        22 |        27 |
   | chr1         |        24 |        30 |
   +--------------+-----------+-----------+
   Unstranded PyRanges object has 4 rows and 3 columns from 1 chromosomes.
   For printing, the PyRanges was sorted on Chromosome.
   Name: b
   +--------------+-----------+-----------+
   | Chromosome   |     Start |       End |
   | (category)   |   (int64) |   (int64) |
   |--------------+-----------+-----------|
   | chr1         |        12 |        32 |
   | chr1         |        14 |        30 |
   +--------------+-----------+-----------+
   Unstranded PyRanges object has 2 rows and 3 columns from 1 chromosomes.
   For printing, the PyRanges was sorted on Chromosome.
   Name: c
   +--------------+-----------+-----------+
   | Chromosome   |     Start |       End |
   | (category)   |   (int64) |   (int64) |
   |--------------+-----------+-----------|
   | chr1         |         8 |        15 |
   | chr1         |        10 |        14 |
   | chr1         |        32 |        34 |
   +--------------+-----------+-----------+
   Unstranded PyRanges object has 3 rows and 3 columns from 1 chromosomes.
   For printing, the PyRanges was sorted on Chromosome.

   >>> pr.count_overlaps(grs)
   +--------------+-----------+-----------+-----------+-----------+-----------+
   | Chromosome   | Start     | End       | a         | b         | c         |
   | (object)     | (int64)   | (int64)   | (int64)   | (int64)   | (int64)   |
   |--------------+-----------+-----------+-----------+-----------+-----------|
   | chr1         | 6         | 8         | 1         | 0         | 0         |
   | chr1         | 8         | 10        | 1         | 0         | 1         |
   | chr1         | 10        | 12        | 2         | 0         | 2         |
   | chr1         | 12        | 14        | 1         | 1         | 2         |
   | ...          | ...       | ...       | ...       | ...       | ...       |
   | chr1         | 24        | 27        | 2         | 2         | 0         |
   | chr1         | 27        | 30        | 1         | 2         | 0         |
   | chr1         | 30        | 32        | 0         | 1         | 0         |
   | chr1         | 32        | 34        | 0         | 0         | 1         |
   +--------------+-----------+-----------+-----------+-----------+-----------+
   Unstranded PyRanges object has 12 rows and 6 columns from 1 chromosomes.
   For printing, the PyRanges was sorted on Chromosome.

   >>> gr = pr.PyRanges(chromosomes=["chr1"] * 4, starts=[0, 10, 20, 30], ends=[10, 20, 30, 40])
   >>> gr
   +--------------+-----------+-----------+
   | Chromosome   |     Start |       End |
   | (category)   |   (int64) |   (int64) |
   |--------------+-----------+-----------|
   | chr1         |         0 |        10 |
   | chr1         |        10 |        20 |
   | chr1         |        20 |        30 |
   | chr1         |        30 |        40 |
   +--------------+-----------+-----------+
   Unstranded PyRanges object has 4 rows and 3 columns from 1 chromosomes.
   For printing, the PyRanges was sorted on Chromosome.

   >>> pr.count_overlaps(grs, gr)
   +--------------+-----------+-----------+-----------+-----------+-----------+
   | Chromosome   |     Start |       End |         a |         b |         c |
   | (category)   |   (int64) |   (int64) |   (int64) |   (int64) |   (int64) |
   |--------------+-----------+-----------+-----------+-----------+-----------|
   | chr1         |         0 |        10 |         1 |         0 |         1 |
   | chr1         |        10 |        20 |         2 |         2 |         2 |
   | chr1         |        20 |        30 |         2 |         2 |         0 |
   | chr1         |        30 |        40 |         0 |         1 |         1 |
   +--------------+-----------+-----------+-----------+-----------+-----------+
   Unstranded PyRanges object has 4 rows and 6 columns from 1 chromosomes.
   For printing, the PyRanges was sorted on Chromosome.