[Bioperl-l] Whither Bio::FeatureIO?

Fields, Christopher J cjfields at illinois.edu
Fri Jul 25 19:59:03 UTC 2014

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).


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?


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...


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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