Whither Bio::FeatureIO?

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Whither Bio::FeatureIO?

George Hartzell-2
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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Re: Whither Bio::FeatureIO?

Fields, Christopher J
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 <[hidden email]> 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
> [hidden email]
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l


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Re: Whither Bio::FeatureIO?

Scott Cain-4
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 <[hidden email]> 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 <[hidden email]> 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
> [hidden email]
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l




--
------------------------------------------------------------------------
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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Re: Whither Bio::FeatureIO?

Fields, Christopher J
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
> [hidden email]
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l




--
------------------------------------------------------------------------
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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Re: Whither Bio::FeatureIO?

Fields, Christopher J
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:


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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
> [hidden email]
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l




--
------------------------------------------------------------------------
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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Re: Whither Bio::FeatureIO?

George Hartzell-2
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.

g.

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Re: Whither Bio::FeatureIO?

Fields, Christopher J
Cool!  I guess I could probably announce this as being released at some point now :)

chris

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 <[hidden email]> 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 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 --gfffile saccharomyces_cerevisiae.gff --outfile saccharomyces_cerevisiae.sorted.gff
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!!!!

g.


On Sat, Aug 30, 2014 at 9:24 PM, George Hartzell <[hidden email]> 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.

g.



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Re: Whither Bio::FeatureIO?

Fields, Christopher J
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).  

chris

On Sep 16, 2014, at 4:53 PM, George Hartzell <[hidden email]> wrote:

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

g.


On Tue, Sep 16, 2014 at 1:41 PM, Fields, Christopher J <[hidden email]> wrote:
Cool!  I guess I could probably announce this as being released at some point now :)

chris

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 <[hidden email]> 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 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 --gfffile saccharomyces_cerevisiae.gff --outfile saccharomyces_cerevisiae.sorted.gff
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!!!!

g.


On Sat, Aug 30, 2014 at 9:24 PM, George Hartzell <[hidden email]> 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.

g.





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