I am trying to convert some codes written in R to Python and part of that conversion process is find classes equivalent to the GRanges and IRanges from the GenomicRanges R package in Python. https://bioconductor.org/packages/release/bioc/vignettes/GenomicRanges/inst/doc/GenomicRangesIntroduction.html#granges-genomic-ranges
I couldn't find any equivalent library written in Python that does the same operations as the aforementioned R classes. There is however pyranges library in Python but it is not as flexible as GRanges and doesn't have IRanges implemented in it. https://github.com/biocore-ntnu/pyranges
For example in R I could add the following in the GRanges class:
gr = GRanges( seq = Rle(DF$chr), ranges = IRanges(DF$Start,DF$End), ref = DF$ref, alt = DF$alt, sampleID=DF$sampleID, seqlengths = chromSize)
However, pyranges don't allow you to add arguments other than (chr, start, end, strand). However, in my case, I need to have the option to add sample_id, seqlengths and other arguments.
Thank you in advance. Best