pyranges.py

import pyranges as pr

gr = pr.PyRanges(chromosomes=["chr1"] * 2 + ["chr2"] * 2, starts=[0, 100, 200, 300], ends=[50, 150, 250, 350], strands=["+", "+", "-", "-"])

gr.spliced_subsequence(0, -75, by="gene")
+--------------+-----------+-----------+--------------+------------+
| Chromosome   |     Start |       End | Strand       |       gene |
| (category)   |   (int64) |   (int32) | (category)   |   (object) |
|--------------+-----------+-----------+--------------+------------|
| chr1         |         0 |        25 | +            |          1 |
| chr2         |       325 |       350 | -            |          2 |
+--------------+-----------+-----------+--------------+------------+
Stranded PyRanges object has 2 rows and 5 columns from 2 chromosomes.
For printing, the PyRanges was sorted on Chromosome and Strand.

gr.spliced_subsequence(-80, -10, by="gene")
+--------------+-----------+-----------+--------------+------------+
| Chromosome   |     Start |       End | Strand       |       gene |
| (category)   |   (int64) |   (int32) | (category)   |   (object) |
|--------------+-----------+-----------+--------------+------------|
| chr1         |        20 |        50 | +            |          1 |
| chr1         |       100 |       140 | +            |          1 |
| chr2         |       210 |       250 | -            |          2 |
| chr2         |       300 |       330 | -            |          2 |
+--------------+-----------+-----------+--------------+------------+
Stranded PyRanges object has 4 rows and 5 columns from 2 chromosomes.
For printing, the PyRanges was sorted on Chromosome and Strand.