10 Turning Ranges into RLEs

Ranges can be turned into dicts of run length encodings with the coverage function:

import pyranges as pr
gr = pr.load_dataset("aorta")
print(gr)

## +--------------+-----------+-----------+------------+-----------+--------------+
## | Chromosome   | Start     | End       | Name       | Score     | Strand       |
## | (category)   | (int64)   | (int64)   | (object)   | (int64)   | (category)   |
## |--------------+-----------+-----------+------------+-----------+--------------|
## | chr1         | 9916      | 10115     | H3K27me3   | 5         | -            |
## | chr1         | 9939      | 10138     | H3K27me3   | 7         | +            |
## | chr1         | 9951      | 10150     | H3K27me3   | 8         | -            |
## | ...          | ...       | ...       | ...        | ...       | ...          |
## | chr1         | 10241     | 10440     | H3K27me3   | 6         | -            |
## | chr1         | 10246     | 10445     | H3K27me3   | 4         | +            |
## | chr1         | 110246    | 110445    | H3K27me3   | 1         | +            |
## +--------------+-----------+-----------+------------+-----------+--------------+
## PyRanges object has 11 sequences from 1 chromosomes.

print(gr.coverage())

## chr1
## +--------+--------+------+------+-----+------+---------+------+-------+-----+---------+-------+
## | Runs   |   9916 |   23 |   12 |   2 |   25 |  ...    |   80 |   114 |   5 |   99801 |   199 |
## |--------+--------+------+------+-----+------+---------+------+-------+-----+---------+-------|
## | Values |      0 |    1 |    2 |   3 |    4 | ...     |    3 |     2 |   1 |       0 |     1 |
## +--------+--------+------+------+-----+------+---------+------+-------+-----+---------+-------+
## Rle of length 110445 containing 22 elements
## Unstranded PyRles object with 1 chromosome.

print(gr.coverage(stranded=True))

## chr1 +
## --
## +--------+--------+------+------+-------+------+------+------+-------+---------+-------+
## | Runs   |   9939 |   14 |   71 |   114 |   14 |   71 |   23 |   199 |   99801 |   199 |
## |--------+--------+------+------+-------+------+------+------+-------+---------+-------|
## | Values |      0 |    1 |    2 |     3 |    2 |    1 |    0 |     1 |       0 |     1 |
## +--------+--------+------+------+-------+------+------+------+-------+---------+-------+
## Rle of length 110445 containing 10 elements
## 
## chr1 -
## --
## +--------+--------+------+------+------+-------+---------+------+------+------+------+-------+
## | Runs   |   9916 |   35 |   27 |   23 |   114 |  ...    |   27 |   23 |   41 |   85 |   114 |
## |--------+--------+------+------+------+-------+---------+------+------+------+------+-------|
## | Values |      0 |    1 |    2 |    3 |     4 | ...     |    3 |    2 |    1 |    2 |     1 |
## +--------+--------+------+------+------+-------+---------+------+------+------+------+-------+
## Rle of length 10440 containing 12 elements
## PyRles object with 2 chromosomes/strand pairs.

You can also create coverage for an any numeric value in your PyRanges:

print(gr.coverage("Score"))

## chr1
## +--------+--------+------+------+-----+------+---------+------+-------+-----+---------+-------+
## | Runs   |   9916 |   23 |   12 |   2 |   25 |  ...    |   80 |   114 |   5 |   99801 |   199 |
## |--------+--------+------+------+-----+------+---------+------+-------+-----+---------+-------|
## | Values |      0 |    5 |   12 |  20 |   25 | ...     |   11 |    10 |   4 |       0 |     1 |
## +--------+--------+------+------+-----+------+---------+------+-------+-----+---------+-------+
## Rle of length 110445 containing 22 elements
## Unstranded PyRles object with 1 chromosome.