Re: [Biopython] biopython module for variant descriptions?

I don't think we have anything like this (yet). Are efforts like VCF
(variant call format) related but separate in your mind?

Peter

On Tue, Oct 31, 2023 at 7:31 PM David Merberg <[email protected]> wrote:

> Hello biopython world,
>
> For my last job, I wrote some python code to categorize and describe
> sequence changes of many types. I used biopython to handle sequences and
> some basic functions like  IO and translation, but I did not find a module
> for reading variants/mutants and applying them to sequences.
>
> Some cases are trivial, but some are not. For example, a small deletion in
> the nucleotide sequence may have no effect on the amino acid corresponding
> to the position of the affected codon, but will affect downstream amino
> acids. Protein changes caused by deletions or insertions of 3, 6, 9 . . .
> nucleotides can also be tricky to calculate.
>
> My question is whether there is a biopython module to read variants in a
> standard format (see for example http://varnomen.hgvs.org/)? Along with
> the variant objects there could be a set of methods to operate on mutated
> sequences. Does the community think that this would be useful if it does
> not already exist?
>
> I implemented many functions for these sorts of operations, but I realized
> soon afterwards that there are probably better ways to do much of it. I
> always wanted to redo the work, but never had time. Now I have time, but am
> not at that job. If it would be useful to the community, I may be able to
> take it on as a contribution to biopython.
>
> A caveat is that I don’t have experience contributing to multi-developer
> projects. I try to write clean, well documented code and I’m familiar with
> the basics of git. So, it’s OK if you’d prefer that I start with something
> smaller (like unit tests or documentation). Just let me know.
>
> Dave Merberg
>
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