<div dir="ltr">Hi Chris,<div><br></div><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>
<div><br></div><div>I haven't looked--what's the state of it now?</div><div><br></div><div>Scott</div><div><br></div></div><div class="gmail_extra"><br><br><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>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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>
<br>
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>
<br>
chris<br>
<div class="HOEnZb"><div class="h5"><br>
On Jul 17, 2014, at 12:23 PM, George Hartzell <<a href="mailto:hartzell@alerce.com">hartzell@alerce.com</a>> wrote:<br>
<br>
> I'm following instructions on the GMOD site to install the Chado schema and related tools.<br>
><br>
> I used cpanm to install BioPerl, which gives me the current version.<br>
><br>
> Various Chado-related tools, e.g. load/bin/gmod_bulk_load_gff3, require Bio::FeatureIO, which is no longer in the BioPerl distribution.<br>
><br>
> I've found a GitHub repo for it, but I can't find any sign of it on CPAN.<br>
><br>
> Has it ever been released?<br>
><br>
> Thanks.<br>
><br>
> g.<br>
><br>
> Sent from a device that makes me type with two fingers.<br>
> _______________________________________________<br>
> Bioperl-l mailing list<br>
> <a href="mailto:Bioperl-l@mailman.open-bio.org">Bioperl-l@mailman.open-bio.org</a><br>
> <a href="http://mailman.open-bio.org/mailman/listinfo/bioperl-l" target="_blank">http://mailman.open-bio.org/mailman/listinfo/bioperl-l</a><br>
<br>
</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <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>