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<p class="MsoNormal">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…<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">chris<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:.5in"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">Lee Katz <lskatz@gmail.com><br>
<b>Date: </b>Wednesday, June 21, 2017 at 8:16 PM<br>
<b>To: </b>Chris Fields <cjfields@illinois.edu><br>
<b>Cc: </b>"<bioperl-l@lists.open-bio.org>" <bioperl-l@mailman.open-bio.org><br>
<b>Subject: </b>Re: [Bioperl-l] Kmer counting<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:.5in">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 :)<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:.5in">On Tue, Jun 20, 2017 at 10:47 PM, Fields, Christopher J <<a href="mailto:cjfields@illinois.edu" target="_blank">cjfields@illinois.edu</a>> wrote:<o:p></o:p></p>
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Hi Lee, <o:p></o:p></p>
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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?<o:p></o:p></p>
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<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
Thanks,<o:p></o:p></p>
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<o:p></o:p></p>
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chris<o:p></o:p></p>
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<o:p></o:p></p>
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<b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">Bioperl-l <bioperl-l-bounces+cjfields=<a href="mailto:illinois.edu@mailman.open-bio.org" target="_blank">illinois.edu@mailman.open-bio.org</a>> on behalf
of Lee Katz <<a href="mailto:lskatz@gmail.com" target="_blank">lskatz@gmail.com</a>><br>
<b>Date: </b>Tuesday, June 6, 2017 at 12:17 PM<br>
<b>To: </b>"<<a href="mailto:bioperl-l@lists.open-bio.org" target="_blank">bioperl-l@lists.open-bio.org</a>>" <<a href="mailto:bioperl-l@mailman.open-bio.org" target="_blank">bioperl-l@mailman.open-bio.org</a>><br>
<b>Subject: </b>[Bioperl-l] Kmer counting</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:1.0in">
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. <o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:.5in">-- <o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:.5in">Lee Katz<o:p></o:p></p>
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