Re: Kmer counting

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 <[email protected]>
Date: Wednesday, June 21, 2017 at 8:16 PM
To: Chris Fields <[email protected]>
Cc: "<[email protected]>" <[email protected]>
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 <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> on behalf of Lee Katz <[email protected]<mailto:[email protected]>>
Date: Tuesday, June 6, 2017 at 12:17 PM
To: "<[email protected]<mailto:[email protected]>>" <[email protected]<mailto:[email protected]>>
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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