9 Finding the closest intervals
With the nearest-method, you can search for the feature in other that is nearest the ones in self.
import pyranges as pr
gr = pr.load_dataset("chipseq")
gr2 = pr.load_dataset("chipseq_background")
print(gr.nearest(gr2, suffix="_Input"))## +--------------+-----------+-----------+------------+-----------+--------------+---------------+-------------+--------------+---------------+----------------+------------+
## | Chromosome | Start | End | Name | Score | Strand | Start_Input | End_Input | Name_Input | Score_Input | Strand_Input | Distance |
## | (category) | (int64) | (int64) | (object) | (int64) | (category) | (int64) | (int64) | (object) | (int64) | (category) | (int64) |
## |--------------+-----------+-----------+------------+-----------+--------------+---------------+-------------+--------------+---------------+----------------+------------|
## | chr1 | 226987592 | 226987617 | U0 | 0 | + | 226987603 | 226987628 | U0 | 0 | - | 0 |
## | chr15 | 26105515 | 26105540 | U0 | 0 | + | 26105493 | 26105518 | U0 | 0 | + | 0 |
## | chr8 | 38747226 | 38747251 | U0 | 0 | - | 38747236 | 38747261 | U0 | 0 | + | 0 |
## | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
## | chrY | 8316773 | 8316798 | U0 | 0 | + | 20557165 | 20557190 | U0 | 0 | + | 2312314 |
## | chrY | 7463444 | 7463469 | U0 | 0 | + | 20557165 | 20557190 | U0 | 0 | + | 3165643 |
## | chrY | 7405376 | 7405401 | U0 | 0 | - | 20557165 | 20557190 | U0 | 0 | + | 3223711 |
## +--------------+-----------+-----------+------------+-----------+--------------+---------------+-------------+--------------+---------------+----------------+------------+
## PyRanges object has 10000 sequences from 24 chromosomes.The nearest method takes a strandedness option, which can either be "same", "opposite" or False/None
print(gr.nearest(gr2, suffix="_Input", strandedness="opposite"))## +--------------+-----------+-----------+------------+-----------+--------------+---------------+-------------+--------------+---------------+----------------+------------+
## | Chromosome | Start | End | Name | Score | Strand | Start_Input | End_Input | Name_Input | Score_Input | Strand_Input | Distance |
## | (category) | (int64) | (int64) | (object) | (int64) | (category) | (int64) | (int64) | (object) | (int64) | (category) | (int64) |
## |--------------+-----------+-----------+------------+-----------+--------------+---------------+-------------+--------------+---------------+----------------+------------|
## | chr1 | 226987592 | 226987617 | U0 | 0 | + | 226987603 | 226987628 | U0 | 0 | - | 0 |
## | chr8 | 38747226 | 38747251 | U0 | 0 | - | 38747236 | 38747261 | U0 | 0 | + | 0 |
## | chr1 | 212609534 | 212609559 | U0 | 0 | + | 212410559 | 212410584 | U0 | 0 | - | 198951 |
## | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
## | chrY | 13517892 | 13517917 | U0 | 0 | - | 11776321 | 11776346 | U0 | 0 | + | 1741547 |
## | chrY | 8010951 | 8010976 | U0 | 0 | - | 20557165 | 20557190 | U0 | 0 | + | 2632551 |
## | chrY | 7405376 | 7405401 | U0 | 0 | - | 20557165 | 20557190 | U0 | 0 | + | 3238126 |
## +--------------+-----------+-----------+------------+-----------+--------------+---------------+-------------+--------------+---------------+----------------+------------+
## PyRanges object has 10000 sequences from 24 chromosomes.The nearest method also takes two variables, namely how and overlap. How can take the values None, "next" and "previous". The default is None, which means that PyRanges looks in both directions. The default is None. The overlap argument is a bool which indicates whether you want to include overlaps or not.
f1 = pr.load_dataset("f1")
print(f1)## +--------------+-----------+-----------+------------+-----------+--------------+
## | Chromosome | Start | End | Name | Score | Strand |
## | (category) | (int64) | (int64) | (object) | (int64) | (category) |
## |--------------+-----------+-----------+------------+-----------+--------------|
## | chr1 | 3 | 6 | interval1 | 0 | + |
## | chr1 | 5 | 7 | interval2 | 0 | - |
## | chr1 | 8 | 9 | interval3 | 0 | + |
## +--------------+-----------+-----------+------------+-----------+--------------+
## PyRanges object has 3 sequences from 1 chromosomes.f2 = pr.load_dataset("f2")
print(f2)## +--------------+-----------+-----------+------------+-----------+--------------+
## | Chromosome | Start | End | Name | Score | Strand |
## | (category) | (int64) | (int64) | (object) | (int64) | (category) |
## |--------------+-----------+-----------+------------+-----------+--------------|
## | chr1 | 1 | 2 | a | 0 | + |
## | chr1 | 6 | 7 | b | 0 | - |
## +--------------+-----------+-----------+------------+-----------+--------------+
## PyRanges object has 2 sequences from 1 chromosomes.print(f2.nearest(f1, strandedness="opposite", how="next"))## +--------------+-----------+-----------+------------+-----------+--------------+-----------+-----------+------------+-----------+--------------+------------+
## | Chromosome | Start | End | Name | Score | Strand | Start_b | End_b | Name_b | Score_b | Strand_b | Distance |
## | (category) | (int64) | (int64) | (object) | (int64) | (category) | (int64) | (int64) | (object) | (int64) | (category) | (int64) |
## |--------------+-----------+-----------+------------+-----------+--------------+-----------+-----------+------------+-----------+--------------+------------|
## | chr1 | 1 | 2 | a | 0 | + | 5 | 7 | interval2 | 0 | - | 4 |
## | chr1 | 6 | 7 | b | 0 | - | 8 | 9 | interval3 | 0 | + | 2 |
## +--------------+-----------+-----------+------------+-----------+--------------+-----------+-----------+------------+-----------+--------------+------------+
## PyRanges object has 2 sequences from 1 chromosomes.print(f2.nearest(f1, strandedness="opposite", how="next", overlap=False))## +--------------+-----------+-----------+------------+-----------+--------------+-----------+-----------+------------+-----------+--------------+------------+
## | Chromosome | Start | End | Name | Score | Strand | Start_b | End_b | Name_b | Score_b | Strand_b | Distance |
## | (category) | (int64) | (int64) | (object) | (int64) | (category) | (int64) | (int64) | (object) | (int64) | (category) | (int64) |
## |--------------+-----------+-----------+------------+-----------+--------------+-----------+-----------+------------+-----------+--------------+------------|
## | chr1 | 1 | 2 | a | 0 | + | 5 | 7 | interval2 | 0 | - | 4 |
## | chr1 | 6 | 7 | b | 0 | - | 8 | 9 | interval3 | 0 | + | 2 |
## +--------------+-----------+-----------+------------+-----------+--------------+-----------+-----------+------------+-----------+--------------+------------+
## PyRanges object has 2 sequences from 1 chromosomes.