12 Methods for manipulating single PyRanges
There are several methods for manipulating the contents of a PyRanges.
merge creates a union of all the intervals in the ranges:
The merge-method also takes the flag count to let you know the number of intervals that were merged.
import pyranges as pr
f1 = pr.data.f1()
print(f1.merge(count=True))## +--------------+-----------+-----------+--------------+-----------+
## | Chromosome | Start | End | Strand | Count |
## | (category) | (int32) | (int32) | (category) | (int32) |
## |--------------+-----------+-----------+--------------+-----------|
## | chr1 | 3 | 6 | + | 1 |
## | chr1 | 8 | 9 | + | 1 |
## | chr1 | 5 | 7 | - | 1 |
## +--------------+-----------+-----------+--------------+-----------+
## Stranded PyRanges object has 3 rows and 5 columns from 1 chromosomes.
## For printing, the PyRanges was sorted on Chromosome and Strand.Cluster finds which intervals overlap, but gives each interval a cluster ID instead of merging them:
import pyranges as pr
f1 = pr.data.f1()
print(f1.cluster())## +--------------+-----------+-----------+------------+-----------+-------+
## | Chromosome | Start | End | Name | Score | +2 |
## | (category) | (int32) | (int32) | (object) | (int64) | ... |
## |--------------+-----------+-----------+------------+-----------+-------|
## | chr1 | 3 | 6 | interval1 | 0 | ... |
## | chr1 | 8 | 9 | interval3 | 0 | ... |
## | chr1 | 5 | 7 | interval2 | 0 | ... |
## +--------------+-----------+-----------+------------+-----------+-------+
## Stranded PyRanges object has 3 rows and 7 columns from 1 chromosomes.
## For printing, the PyRanges was sorted on Chromosome and Strand.
## 2 hidden columns: Strand, Clusterprint(f1.cluster(strand=True))## +--------------+-----------+-----------+------------+-----------+-------+
## | Chromosome | Start | End | Name | Score | +2 |
## | (category) | (int32) | (int32) | (object) | (int64) | ... |
## |--------------+-----------+-----------+------------+-----------+-------|
## | chr1 | 3 | 6 | interval1 | 0 | ... |
## | chr1 | 8 | 9 | interval3 | 0 | ... |
## | chr1 | 5 | 7 | interval2 | 0 | ... |
## +--------------+-----------+-----------+------------+-----------+-------+
## Stranded PyRanges object has 3 rows and 7 columns from 1 chromosomes.
## For printing, the PyRanges was sorted on Chromosome and Strand.
## 2 hidden columns: Strand, Clusterprint(f1.cluster(slack=2, strand=True, count=True))## +--------------+-----------+-----------+------------+-----------+-------+
## | Chromosome | Start | End | Name | Score | +3 |
## | (category) | (int32) | (int32) | (object) | (int64) | ... |
## |--------------+-----------+-----------+------------+-----------+-------|
## | chr1 | 3 | 6 | interval1 | 0 | ... |
## | chr1 | 8 | 9 | interval3 | 0 | ... |
## | chr1 | 5 | 7 | interval2 | 0 | ... |
## +--------------+-----------+-----------+------------+-----------+-------+
## Stranded PyRanges object has 3 rows and 8 columns from 1 chromosomes.
## For printing, the PyRanges was sorted on Chromosome and Strand.
## 3 hidden columns: Strand, Cluster, CountIt also takes an flag count.
Both cluster and merge take the argument slack, so that you can merge features which are not directly overlapping. If you set slack to -1 you avoid merging bookended features. To only merge features overlapping by at least X, set slack to -X.
To cluster or merge only those rows which have the same values for a certain column, you can use the argument by to cluster and merge.
import pyranges as pr
gr = pr.data.ensembl_gtf()
print(gr)## +--------------+------------+--------------+-----------+-----------+-------+
## | Chromosome | Source | Feature | Start | End | +23 |
## | (category) | (object) | (category) | (int32) | (int32) | ... |
## |--------------+------------+--------------+-----------+-----------+-------|
## | 1 | havana | gene | 11868 | 14409 | ... |
## | 1 | havana | transcript | 11868 | 14409 | ... |
## | 1 | havana | exon | 11868 | 12227 | ... |
## | 1 | havana | exon | 12612 | 12721 | ... |
## | ... | ... | ... | ... | ... | ... |
## | 1 | havana | gene | 1173055 | 1179555 | ... |
## | 1 | havana | transcript | 1173055 | 1179555 | ... |
## | 1 | havana | exon | 1179364 | 1179555 | ... |
## | 1 | havana | exon | 1173055 | 1176396 | ... |
## +--------------+------------+--------------+-----------+-----------+-------+
## Stranded PyRanges object has 2,446 rows and 28 columns from 1 chromosomes.
## For printing, the PyRanges was sorted on Chromosome and Strand.
## 23 hidden columns: Score, Strand, Frame, gene_biotype, gene_id, gene_name, gene_source, ... (+ 16 more.)print(gr.cluster(by="gene_id"))## +--------------+----------------+----------------+-----------+-------+
## | Chromosome | Source | Feature | Start | +25 |
## | (category) | (object) | (category) | (int32) | ... |
## |--------------+----------------+----------------+-----------+-------|
## | 1 | ensembl_havana | gene | 1173883 | ... |
## | 1 | havana | transcript | 1173883 | ... |
## | 1 | havana | exon | 1173883 | ... |
## | 1 | havana | transcript | 1173902 | ... |
## | ... | ... | ... | ... | ... |
## | 1 | ensembl_havana | stop_codon | 450739 | ... |
## | 1 | ensembl_havana | CDS | 450742 | ... |
## | 1 | ensembl_havana | start_codon | 451675 | ... |
## | 1 | ensembl_havana | five_prime_utr | 451678 | ... |
## +--------------+----------------+----------------+-----------+-------+
## Stranded PyRanges object has 2,446 rows and 29 columns from 1 chromosomes.
## For printing, the PyRanges was sorted on Chromosome and Strand.
## 25 hidden columns: End, Score, Strand, Frame, gene_biotype, gene_id, gene_name, ... (+ 18 more.)If you want to split a pyrange on the overlapping intervals, you can use split:
import pyranges as pr
f1 = pr.data.f1()
print(f1)## +--------------+-----------+-----------+------------+-----------+--------------+
## | Chromosome | Start | End | Name | Score | Strand |
## | (category) | (int32) | (int32) | (object) | (int64) | (category) |
## |--------------+-----------+-----------+------------+-----------+--------------|
## | chr1 | 3 | 6 | interval1 | 0 | + |
## | chr1 | 8 | 9 | interval3 | 0 | + |
## | chr1 | 5 | 7 | interval2 | 0 | - |
## +--------------+-----------+-----------+------------+-----------+--------------+
## Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes.
## For printing, the PyRanges was sorted on Chromosome and Strand.print(f1.split())## +--------------+-----------+-----------+------------+
## | Chromosome | Start | End | Strand |
## | (object) | (int32) | (int32) | (object) |
## |--------------+-----------+-----------+------------|
## | chr1 | 3 | 6 | + |
## | chr1 | 8 | 9 | + |
## | chr1 | 5 | 7 | - |
## +--------------+-----------+-----------+------------+
## Stranded PyRanges object has 3 rows and 4 columns from 1 chromosomes.
## For printing, the PyRanges was sorted on Chromosome and Strand.five_end finds the starts of the regions (taking direction of transcription
into account).
f1.five_end()
print(f1.five_end())## +--------------+-----------+-----------+------------+-----------+--------------+
## | Chromosome | Start | End | Name | Score | Strand |
## | (category) | (int32) | (int32) | (object) | (int64) | (category) |
## |--------------+-----------+-----------+------------+-----------+--------------|
## | chr1 | 3 | 4 | interval1 | 0 | + |
## | chr1 | 8 | 9 | interval3 | 0 | + |
## | chr1 | 6 | 7 | interval2 | 0 | - |
## +--------------+-----------+-----------+------------+-----------+--------------+
## Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes.
## For printing, the PyRanges was sorted on Chromosome and Strand.three_end finds the ends of the regions (taking direction of transcription into account).
f1.three_end()
print(f1.three_end())## +--------------+-----------+-----------+------------+-----------+--------------+
## | Chromosome | Start | End | Name | Score | Strand |
## | (category) | (int32) | (int32) | (object) | (int64) | (category) |
## |--------------+-----------+-----------+------------+-----------+--------------|
## | chr1 | 5 | 6 | interval1 | 0 | + |
## | chr1 | 8 | 9 | interval3 | 0 | + |
## | chr1 | 5 | 6 | interval2 | 0 | - |
## +--------------+-----------+-----------+------------+-----------+--------------+
## Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes.
## For printing, the PyRanges was sorted on Chromosome and Strand.extend (also aliased slack) extends the starts and ends of your interval:
print(f1.slack(5))## +--------------+-----------+-----------+------------+-----------+--------------+
## | Chromosome | Start | End | Name | Score | Strand |
## | (category) | (int32) | (int32) | (object) | (int64) | (category) |
## |--------------+-----------+-----------+------------+-----------+--------------|
## | chr1 | 0 | 11 | interval1 | 0 | + |
## | chr1 | 3 | 14 | interval3 | 0 | + |
## | chr1 | 0 | 12 | interval2 | 0 | - |
## +--------------+-----------+-----------+------------+-----------+--------------+
## Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes.
## For printing, the PyRanges was sorted on Chromosome and Strand.print(f1.slack({"5": 2, "3": -1}))## +--------------+-----------+-----------+------------+-----------+--------------+
## | Chromosome | Start | End | Name | Score | Strand |
## | (category) | (int32) | (int32) | (object) | (int64) | (category) |
## |--------------+-----------+-----------+------------+-----------+--------------|
## | chr1 | 1 | 5 | interval1 | 0 | + |
## | chr1 | 6 | 8 | interval3 | 0 | + |
## | chr1 | 6 | 9 | interval2 | 0 | - |
## +--------------+-----------+-----------+------------+-----------+--------------+
## Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes.
## For printing, the PyRanges was sorted on Chromosome and Strand.window splits your data into windows:
exons = pr.data.exons()
print(exons)## +--------------+-----------+-----------+-------+
## | Chromosome | Start | End | +3 |
## | (category) | (int32) | (int32) | ... |
## |--------------+-----------+-----------+-------|
## | chrX | 135721701 | 135721963 | ... |
## | chrX | 135574120 | 135574598 | ... |
## | chrX | 47868945 | 47869126 | ... |
## | chrX | 77294333 | 77294480 | ... |
## | ... | ... | ... | ... |
## | chrY | 15409586 | 15409728 | ... |
## | chrY | 15478146 | 15478273 | ... |
## | chrY | 15360258 | 15361762 | ... |
## | chrY | 15467254 | 15467278 | ... |
## +--------------+-----------+-----------+-------+
## Stranded PyRanges object has 1,000 rows and 6 columns from 2 chromosomes.
## For printing, the PyRanges was sorted on Chromosome and Strand.
## 3 hidden columns: Name, Score, Strandprint(exons.window(5))## +--------------+-----------+-----------+-------+
## | Chromosome | Start | End | +3 |
## | (category) | (int32) | (int32) | ... |
## |--------------+-----------+-----------+-------|
## | chrX | 135721701 | 135721706 | ... |
## | chrX | 135721706 | 135721711 | ... |
## | chrX | 135721711 | 135721716 | ... |
## | chrX | 135721716 | 135721721 | ... |
## | ... | ... | ... | ... |
## | chrY | 15467259 | 15467264 | ... |
## | chrY | 15467264 | 15467269 | ... |
## | chrY | 15467269 | 15467274 | ... |
## | chrY | 15467274 | 15467278 | ... |
## +--------------+-----------+-----------+-------+
## Stranded PyRanges object has 61,268 rows and 6 columns from 2 chromosomes.
## For printing, the PyRanges was sorted on Chromosome and Strand.
## 3 hidden columns: Name, Score, StrandIf you want to all windows to start at a multiple of window_size, use the tile function:
You can use the overlap flag to see how many basepairs each tile overlapped with the underlying interval.
print(exons.tile(5))## +--------------+-----------+-----------+-------+
## | Chromosome | Start | End | +3 |
## | (category) | (int32) | (int32) | ... |
## |--------------+-----------+-----------+-------|
## | chrX | 135721700 | 135721705 | ... |
## | chrX | 135721705 | 135721710 | ... |
## | chrX | 135721710 | 135721715 | ... |
## | chrX | 135721715 | 135721720 | ... |
## | ... | ... | ... | ... |
## | chrY | 15467260 | 15467265 | ... |
## | chrY | 15467265 | 15467270 | ... |
## | chrY | 15467270 | 15467275 | ... |
## | chrY | 15467275 | 15467280 | ... |
## +--------------+-----------+-----------+-------+
## Stranded PyRanges object has 61,643 rows and 6 columns from 2 chromosomes.
## For printing, the PyRanges was sorted on Chromosome and Strand.
## 3 hidden columns: Name, Score, Strandprint(exons.tile(5, overlap=True))## +--------------+-----------+-----------+-------+
## | Chromosome | Start | End | +4 |
## | (category) | (int32) | (int32) | ... |
## |--------------+-----------+-----------+-------|
## | chrX | 135721700 | 135721705 | ... |
## | chrX | 135721705 | 135721710 | ... |
## | chrX | 135721710 | 135721715 | ... |
## | chrX | 135721715 | 135721720 | ... |
## | ... | ... | ... | ... |
## | chrY | 15467260 | 15467265 | ... |
## | chrY | 15467265 | 15467270 | ... |
## | chrY | 15467270 | 15467275 | ... |
## | chrY | 15467275 | 15467280 | ... |
## +--------------+-----------+-----------+-------+
## Stranded PyRanges object has 61,643 rows and 7 columns from 2 chromosomes.
## For printing, the PyRanges was sorted on Chromosome and Strand.
## 4 hidden columns: Name, Score, Strand, TileOverlap