[Biopython-dev] Operations on kmers?

Michiel de Hoon mjldehoon at yahoo.com
Fri Feb 3 08:15:05 UTC 2017

Hi Alexey,Thank you for your offer to contribute to Biopython.
I would suggest to write to the biopython users mailing list to find out how many people would be interested in using the module. If there are many, we can include it; if there are few, then it may be better to keep it separate. If it's included in Biopython, I think one of the existing modules could be used, perhaps Bio.Seq or Bio.motifs. Bio.Statistics is not really developed and perhaps should be removed altogether, and Bio.Cluster is about clustering rather than sequence analysis.Best,-Michiel 

    On Friday, February 3, 2017 2:14 PM, Alexey Morozov <alexeymorozov1991 at gmail.com> wrote:

 I've written a little library for k-mer based analyses, and eventually decided to upload it to PyPI. Guess what? There are several modules for that (https://pypi.python.org/pypi? %3Aaction=search&term=kmer& submit=search), including my own (kmers). Is there a chance one of those can make it to Biopython? It's usually better to have a singe universally available library than a bunch of incompatiblble ones.
I'm willing to work on it, probably in cooperation with folks that made other packages, but I don't have a slightest idea whether it's gonna be accepted to Biopython. k-mers are still somewhat obscure, after all. If it is, where, in your opinion, does it belong? A separate Bio.Kmers module, a submodule of Bio.Statistics or Bio.Cluster? Something else?

Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.

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