[Bioperl-l] Kmer counting

[Fields, Christopher J]

It’s probably best as a standalone library, particularly if it’s very focused on this specific need.  Saying that, I could see you adding code or a simple example script that would (as an example) read in sequences via Bioperl and perform kmer-based analyses on them.  Not that reading FASTQ via bioperl is very fast…

chris

From: Lee Katz <lskatz at gmail.com>
Date: Wednesday, June 21, 2017 at 8:16 PM
To: Chris Fields <cjfields at illinois.edu>
Cc: "<bioperl-l at lists.open-bio.org>" <bioperl-l at mailman.open-bio.org>
Subject: Re: [Bioperl-l] Kmer counting

Yes this is what I mean but having looked at what I might need to change to make it bioperl-esque, I am thinking of just keeping it as standalone.  I appreciate what you are offering but I think for now I will keep it as-is until I get a little more free time :)

On Tue, Jun 20, 2017 at 10:47 PM, Fields, Christopher J <cjfields at illinois.edu<mailto:cjfields at illinois.edu>> wrote:
Hi Lee,

Missed this email, apologies.  This primarily depends on how it would fit within Bioperl; since it’s primarily stand-alone and doesn’t require Bioperl, it probably doesn’t need to be in core.  We can certainly include it in the other Bio* distributions on the github page if needed (and add you to the repo as primary admin).  Is this what you mean?

Thanks,

chris

From: Bioperl-l <bioperl-l-bounces+cjfields=illinois.edu at mailman.open-bio.org<mailto:illinois.edu at mailman.open-bio.org>> on behalf of Lee Katz <lskatz at gmail.com<mailto:lskatz at gmail.com>>
Date: Tuesday, June 6, 2017 at 12:17 PM
To: "<bioperl-l at lists.open-bio.org<mailto:bioperl-l at lists.open-bio.org>>" <bioperl-l at mailman.open-bio.org<mailto:bioperl-l at mailman.open-bio.org>>
Subject: [Bioperl-l] Kmer counting

Hi, I was wondering if my module Bio::Kmer fits with bioperl. I put it onto cpan and have basic unit tests, but it doesn't inherit anything from bioperl.



--
Lee Katz
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