Questions about the PyRanges library.
Questions about the PyRanges library (https://doi.org/10.1093/bioinformatics/btz615).
pyranges is a GenomicRanges implementation for Python built on top of pandas.
Questions tagged [pyranges]
8 questions
3
votes
1 answer
Difference between overlap and intersect methods in Pyranges
Pyranges class from similarly named package has two methods with slightly different functionality:
intersect and
overlap.
Intersect method description is quite similar to overlap's one: Return overlapping subintervals. vs Return overlapping…
AlexShein
- 166
- 1
- 13
2
votes
1 answer
How to convert chromosome name to same format in pyranges before performing a join
I have multiple .bed files and I want to perform join, intersection etc. operation on them. I am using pyranges library to read the .bed files and perform these operations. As .bed files allows naming chromosome with or without "chr" prefix, I would…
srgothi92
- 55
- 4
2
votes
2 answers
pythonic equivalent to reduce() in R GRanges - how to collapse ranged data?
In R (albeit longwinded):
Here is a test data.frame
df <- data.frame(
"CHR" = c(1,1,1,2,2),
"START" = c(100, 200, 300, 100, 400),
"STOP" = c(150,350,400,500,450)
)
First I make GRanges object:
gr <- GenomicRanges::GRanges(
seqnames =…
mbyvcm
- 141
- 2
- 12
1
vote
1 answer
Faster PyRanges Generation in Python
I have a list of starting coordinates all on the same chromosome for features of fixed size and I am trying to generate a PyRanges object.
I timed the generation of the PyRanges object on a list of 125 coordinates and it took around 3.5ms. This…
Fabrizio
- 1,138
- 4
- 18
- 41
1
vote
1 answer
Using pyranges library, How to check if a chromosome position is contained in any interval?
I have a .vcf file containing variants information and a .bed file containing region studied information. I am using pyranges library to read the .bed file. I want to filter out all the variants in .vcf file that lies in the region studied intervals…
srgothi92
- 55
- 4
1
vote
2 answers
Finding overlaps between millions of ranges/intervals
I am trying to find pairs of intervals that overlap by at least some minimum overlap length that is set by the user. The intervals are from this pandas dataframe:
import pandas as pds
print(df1.head())
print(df1.tail())
query_id start_pos …
Michael
- 13
- 4
0
votes
0 answers
python PyRanges warning message when the intersection is empty
Dear python community,
Im trying to figure out why im getting the following warning message when I try to find the intersection between two pyrange dataframes whenever the resulting intersection is empty:
the code is the following:
intersection =…
user3289556
- 155
- 2
- 11
0
votes
1 answer
Pyranges gets indices if there are overlaps and NaN if not
I'm trying to use pyranges for some efficient implementation but it's very limited and inflexible compared to R GenomicRanges.
Let's say if I have two Pyranges Tables: pr1 & pr2. I want to get the indices of the overlaping rows of pr1 in pr2 and, in…
Moses Stamboulian
- 11
- 2