[Bioperl-l] Whither Bio::FeatureIO?

Sun Aug 31 01:57:46 UTC 2014

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:

   https://metacpan.org/pod/Bio::FeatureIO

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.

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.

chris

On Jul 25, 2014, at 2:59 PM, Fields, Christopher J <cjfields at illinois.edu<mailto:cjfields at illinois.edu>> wrote:

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).

chris

On Jul 24, 2014, at 1:53 PM, Scott Cain <scott at scottcain.net<mailto:scott at scottcain.net>> wrote:

Hi Chris,

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.

I haven't looked--what's the state of it now?

Scott

On Thu, Jul 17, 2014 at 5:58 PM, Fields, Christopher J <cjfields at illinois.edu<mailto:cjfields at illinois.edu>> wrote:
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.

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...

chris

On Jul 17, 2014, at 12:23 PM, George Hartzell <hartzell at alerce.com<mailto:hartzell at alerce.com>> wrote:

> I'm following instructions on the GMOD site to install the Chado schema and related tools.
>
> I used cpanm to install BioPerl, which gives me the current version.
>
> Various Chado-related tools, e.g. load/bin/gmod_bulk_load_gff3, require Bio::FeatureIO, which is no longer in the BioPerl distribution.
>
> I've found a GitHub repo for it, but I can't find any sign of it on CPAN.
>
> Has it ever been released?
>
> Thanks.
>
> g.
>
> Sent from a device that makes me type with two fingers.
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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