pybedtools
pybedtools copied to clipboard
daler
Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
Hi there, I've made an enhancement to pybedtools that adds support for the CSI index. The default TBI index fails for chromosomes larger than 512 Mbp, such as barley's chromosome...
Hi, First of all - thank you for your amazing work. pybedtools has been super useful for my research so far and I am very grateful. I'm trying to run...
This PR fixes https://github.com/daler/pybedtools/issues/376 and support for polars dataframes. Users can now convert a `BedTool` object to a polars dataframe using the `to_polars_dataframe` method, and create a `BedTool` object from...
## Integration with other packages If `pybedtools.pkg_integration = True`, then: 1. Iterating over SAM or BAM yields `pysam.AlignedRead` objects 2. Iterating over VCF yields `cyvcf2.Variant` objects 3. (?) Iterating over...
The need for (or the convenience of) a function such as `intersect_dfs` is demonstrated in this [StackExchange thread](https://bioinformatics.stackexchange.com/questions/9015/how-to-do-bedtools-intersection-using-pandas-alone/15181#15181). Often your workflow is pandas' based but at some point, during that...
`BedTool.genome_coverage` sometimes returns bedGraph-like output, sometimes not. In fact, by default, it doesn't return a valid BED-ish format file. See #110, #111, #112. _note to future self: this prob needs...
I am trying to run something like this: ``` $ cat a.bed chr1 10 20 a1 1 - $ cat b1.bed chr1 5 6 b1.1 1 - chr1 30 40...
Im interested in the handling of indels in VCF files . I have created a bedtool from VCF that includes an indel with reference length 18 but the interval has...
For streaming intersections of moderate-sized files (say, >5000 features), the following blocks:: ``` z = a.intersect(b, stream=True).intersect(c, stream=True) len(z) ``` The schematic below shows what's happening with stdin/stdout and pipes....
Imagine we have two bed files, and we do this: ``` python z = x.intersect(y, wao=True) ``` The resulting file could look like this, is incorrectly guessed to be SAM...