[Bioperl-l] Whither Bio::FeatureIO?

Fields, Christopher J cjfields at illinois.edu
Tue Sep 16 22:39:15 UTC 2014

It *might* be possible to set this up on Travis-CI independently on Bio::FeatureIO, which would be beneficial from a testing viewpoint (as we need to track what works w/ refactored FeatureIO vs what doesn’t).

I suppose what we need to check with a refactor (master branch) is:

1) Maintaining a sane amount of compat. with Chado.  ‘Sane' meaning Bio::SF::Annotated will need to be chucked or completely reimplemented from scratch, as it is much less than sane now
2) If needed having a concurrently developed version of Chado to make it work.

It may not require much on #2 if Chado isn’t reliant on some of the less API-friendly parts of Bio::SF::Annotated (namely the heavy annotation associated with it).


On Sep 16, 2014, at 4:53 PM, George Hartzell <hartzell.george at gene.com<mailto:hartzell.george at gene.com>> wrote:

@scott, do you have test setup for the GMOD stuff?



On Tue, Sep 16, 2014 at 1:41 PM, Fields, Christopher J <cjfields at illinois.edu<mailto:cjfields at illinois.edu>> wrote:
Cool!  I guess I could probably announce this as being released at some point now :)


PS - I may have a decent test environment set up for longer-term evaluation, but it would be nice to see if we can get something working with travis-ci or a smoker setup, just so I can check whether the main branch refactoring is clobbering chado (as I suspect it is).

On Sep 16, 2014, at 1:50 PM, George Hartzell <hartzell.george at gene.com<mailto:hartzell.george at gene.com>> wrote:

Hi All,

It took a while, but I was finally able to run my little litmus test and the good news is that it appears to pass.

I modified my ansible playbook that implements the steps described in INSTALL.Chado<https://svn.code.sf.net/p/gmod/svn/schema/trunk/chado/INSTALL.Chado> so that it uses the version of Bio::FeatureIO that is now on CPAN instead of pulling the github master.

The resulting installation ran to completion and then was able to load the yeast gff3 file:

cp /vagrant/saccharomyces_cerevisiae.gff .
gmod_gff3_preprocessor.pl<http://gmod_gff3_preprocessor.pl/> --gfffile saccharomyces_cerevisiae.gff --outfile saccharomyces_cerevisiae.sorted.gff
gmod_bulk_load_gff3.pl<http://gmod_bulk_load_gff3.pl/> --organism yeast  --gfffile saccharomyces_cerevisiae.gff.sorted

and the resulting database seems to be stitched together reasonably (though I’m not a particularly informed judge of its character).

@chris thanks for the help on this!!!!



On Sat, Aug 30, 2014 at 9:24 PM, George Hartzell <hartzell at alerce.com<mailto:hartzell at alerce.com>> wrote:
Fields, Christopher J writes:
 > 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.

I can't do anything until Tuesday, but will be happy to run it through
the standard Chado build process when I get back to work.

Thanks for digging into it.


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