[Bioperl-l] Whither Bio::FeatureIO?

Scott Cain scott at scottcain.net
Thu Jul 24 18:53:26 UTC 2014

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> 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> 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.
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at mailman.open-bio.org
> > http://mailman.open-bio.org/mailman/listinfo/bioperl-l

Scott Cain, Ph. D.                                   scott at scottcain dot
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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