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<div>Just a quick update on this: I released a separate Bio::FeatureIO release to CPAN that represents the code split out from the core modules:</div>
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<div> <a href="https://metacpan.org/pod/Bio::FeatureIO">https://metacpan.org/pod/Bio::FeatureIO</a></div>
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<div>I had to do some cleanup to get code to work and tests passing with some sanity. A *lot* of things were not passing tests when we moved this over. </div>
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<div>This should represent what was last working with Chado though. However, I haven’t officially announced anything yet b/c I would like to shake bugs out of it. Can either of you try this out on a Chado run to make sure everything is up to snuff (or at least
point out issues)? Time depending, I would like to get something running on (for instance) Travis-CI, maybe including some optional Chado-related stuff. This would also help so that we can work on merging what has been done on master so that these pass the
same tests.</div>
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<div>chris</div>
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<div>On Jul 25, 2014, at 2:59 PM, Fields, Christopher J <<a href="mailto:cjfields@illinois.edu">cjfields@illinois.edu</a>> wrote:</div>
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The commit history is all there I believe; we could simply commit a tag pointing to the last commit prior to all the major code changes and make that a separate release (probably with a separate version, 1.7 at least).
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<div>chris</div>
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<div>On Jul 24, 2014, at 1:53 PM, Scott Cain <<a href="mailto:scott@scottcain.net">scott@scottcain.net</a>> wrote:</div>
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<div dir="ltr">Hi Chris,
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<div>I almost forgot about this thread. Yes, there are still tools in the GMOD distribution (including the GFF bulk loader) that use Bio::FeatureIO. I'm still using 1.6.901 for most things, so I've not been bitten by its being gone. A distribution on CPAN
would probably be best, and a corresponding new release of Chado (because I have all the time in the world to work on that!) to go with it.</div>
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<div>I haven't looked--what's the state of it now?</div>
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<div>Scott</div>
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<div class="gmail_quote">On Thu, Jul 17, 2014 at 5:58 PM, Fields, Christopher J <span dir="ltr">
<<a href="mailto:cjfields@illinois.edu" target="_blank">cjfields@illinois.edu</a>></span> wrote:<br>
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It’s been moved to a separate github distribution, namely Bio-FeatureIO, but it was also being largely rewritten as the original implementation was never completed. We can probably set up a branch with the relevant version of the code that should work with
the script.<br>
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Scott, is this the recommended way of loading Chado data in still? Do we need a working version of Bio::FeatureIO on CPAN so it’s available? For some reason I thought users started going with Bio::Chado::Schema...<br>
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chris<br>
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On Jul 17, 2014, at 12:23 PM, George Hartzell <<a href="mailto:hartzell@alerce.com">hartzell@alerce.com</a>> wrote:<br>
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> I'm following instructions on the GMOD site to install the Chado schema and related tools.<br>
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> I used cpanm to install BioPerl, which gives me the current version.<br>
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> Various Chado-related tools, e.g. load/bin/gmod_bulk_load_gff3, require Bio::FeatureIO, which is no longer in the BioPerl distribution.<br>
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> I've found a GitHub repo for it, but I can't find any sign of it on CPAN.<br>
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> Has it ever been released?<br>
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> Thanks.<br>
><br>
> g.<br>
><br>
> Sent from a device that makes me type with two fingers.<br>
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-- <br>
------------------------------------------------------------------------<br>
Scott Cain, Ph. D. scott at scottcain dot net<br>
GMOD Coordinator (<a href="http://gmod.org/">http://gmod.org/</a>) 216-392-3087<br>
Ontario Institute for Cancer Research </div>
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