Questions tagged [pybedtools]
pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python.
6
questions
1
vote
1answer
32 views
How to detect bedtools version used by pybedtools (in order to correctly preserve strand information when merging gtf records)
I have issues working with pybedtools due to strand information being lost after extracting and merging transcript coordinates from a gtf file.
It seems that the solution to preserve strand ...
0
votes
1answer
50 views
Summing two columns where they share interval overlap
I have two bed files where each column has a numeric score. I want to sum these numbers where there is overlap between the two bed files. How do I do that? Also, I am only interested in the score in ...
7
votes
4answers
1k views
How to do `bedtools intersection` using pandas alone?
I have two pandas Dataframes, using python3.x:
...
1
vote
1answer
114 views
How to efficiently extract coordinates from a `pybedtools.Interval`?
I'm using pybedtools to process data, and at some point, I loop over a BedTool object and use unpacking to extract coordinates from the ...
4
votes
1answer
67 views
How to use variables while calling pybedtools
I am trying to use bedtools and fetch sequences from a whole genome fasta file inside the script I get region coordinates as variables.
For example:
...
2
votes
1answer
824 views
How to split bedfile into non-overlapping regions and compute aggregation function on duplicate segments
I have a bed-like file in which I have several overlapping regions with associated features. I want to split the overlapping regions into disjoint regions in order to process the file (e.g. with ...
