Re: [Gmod-tripal] exporting GFF file

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Re: [Gmod-tripal] exporting GFF file

Scott Cain
Hi Eric,

I cc'ed both the Tripal mailing list (since this is where the discussion started) and the schema mailing list since it is a more general topic as well.

The tables in Chado that have gff in the name have to do with aspects of processing GFF as it's loaded and won't be of any use dumping GFF out.  There are a few views that would help though.  Specifically, I used the gff3view when writing the gff_string method of Bio::DB::Das::Chado::Segment::Feature, which I used for supporting GBrowse's GFF dumping functionality (at least, I'm pretty sure that's what I did; it was a long time ago).  That is a reasonable place to start.

Another thing you could look at is the bulkfiles functionality of GMODTools, which is distributed with the Chado installer.  It has a steeper learning curve (and I'm not the one who wrote the documentation :-), but once it's set up and configured it would probably be faster at generating things like GFF and fasta files on a whole-organism basis.

Scott



On Thu, Jul 25, 2013 at 1:26 PM, Eric Rasche <[hidden email]> wrote:
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi Scott,

Yes, absolutely via cached/pre-generated GFFs. I saw some GFF related
functions in the chado schema, is there anywhere I should start looking
for such functions when I go to write the download module?

Most of the artemis issue was that it required us to patch in SSL
support for database connections like Chado. That has now been submitted
as a merge request to Sanger.

Cheers,
Eric

On 07/25/2013 12:19 PM, Scott Cain wrote:
> Hi Eric,
>
> It makes a lot of sense to have a "download GFF" button on an organism's
> page, but I would think it would be better to have that has pre-generated
> GFF, since it could be quite a drain on the database's resources to
> generate a whole organism's GFF on the fly.
>
> I'm glad you got the Artemis stuff sorted out.
>
> Scott
>
>
>
> On Thu, Jul 25, 2013 at 1:07 PM, Eric Rasche <[hidden email]> wrote:
>
> Hi Scott,
>
> Well, this was posted a while ago, and since then I've managed to get
> Artemis to talk to Chado, which solves my problem in another manner.
>
> If GBrowse has an export option then that would have otherwise answered
> my question. We deployed a gbrowse instance, but haven't used it yet.
>
> What I had been imagining was simply a "Download GFF3" button on the
> organism pages, allowing for a one click download of that organism's
> file. However, since gbrowse does this, writing that feature again
> probably wouldn't be very useful.
>
>
> Cheers,
> Eric Rasche
>
> On 07/25/2013 12:02 PM, Scott Cain wrote:
>>>> Hi Eric,
>>>>
>>>> I'm not sure how generically useful that would be (though I can't speak
> for
>>>> the Tripal developers).  GBrowse has a GFF3 export option, and there are
>>>> command line tools as well.  What would you want in terms of a user
>>>> interface?
>>>>
>>>> Scott
>>>>
>>>>
>>>>
>>>> On Tue, Jul 23, 2013 at 12:09 PM, Eric Rasche <[hidden email]>
> wrote:
>>>>
>>>> Hello all,
>>>>
>>>>  Is there currently any plans for functionality to export a GFF3 file
>>>> from tripal?
>>>>
>>>> Since I'm having issues getting WebApollo to work with Chado, we'll
>>>> continue to be editing these genomes in Artemis.
>>>>
>>>> Cheers,
>>>> Eric
>>>>
>>>>
>>>>>
>>>>>
>>>>>
> ------------------------------------------------------------------------------
>>>>> See everything from the browser to the database with AppDynamics
>>>>> Get end-to-end visibility with application monitoring from AppDynamics
>>>>> Isolate bottlenecks and diagnose root cause in seconds.
>>>>> Start your free trial of AppDynamics Pro today!
>>>>>
> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk
>>>>> _______________________________________________
>>>>> Gmod-tripal mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>
>>>>
>>>>
>>>>
>>
>
>
>
- --
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843
<a href="tel:404-692-2048" value="+14046922048">404-692-2048
[hidden email]
[hidden email]
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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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Re: [Gmod-tripal] exporting GFF file

Lacey-Anne Sanderson-3
Hi Eric,

If I were going to add exporting of GFF3 to Tripal I would create a new views bulk data export plugin like we did for exporting FASTA files. This would allow you to add a data export display to any feature view of style GFF3 which would give you a feed button exporting all the current features in the view (including exposed filtering :D) in GFF3 format. I would code this up myself if I weren't on maternity leave with my time dictated by a cute but very demanding boss :p

The advantages of this are:
 -  re-usability (it's generic enough for any Tripal website and can be used on multiple views in your own site with many different existing filters)
 -  allows you to export any set of features in a Tripal chado database by adding already existing filters to a feature view (i.e.: easy to say export all features in a given analysis/library or of a given type or from a given organism -including any combination of such options :))
 - requires minimal coding since the infrastructure is already there (the code to get the features to be exported, display filtering options to the user/admin, etc. is already done)
 - hooks into the views module allowing it to be used not just on feature views but also materialized views created through Tripal that can provide the necessary feature fields (allows you to do your own filtering using SQL if there are not the correct views filters yet making for the ultimate in flexibility)
  - probably many others I can't think of at this time :)

I would start by looking at how my marked-up FASTA export plugin was coded since it retrieves the parent features as well. It's contained in my KP Feature Export module (https://drupal.org/sandbox/laceysanderson/1341380). Specifically, you want to look at plugins/views_data_export_style_export_kaspar.inc. This file contains all the code needed to make the export style. Other then that you just need to register the export style in the .module file using hook views_data_export_styles (you can see an example in my module and I added code at the bottom of this email showing how you would add the registration to my own module).

I would love it if you submitted this export type as a patch to my module (I would of course give you recognition on the info page of the module :)) since it would be a Very useful export type to have (I would maintain it in the future as regular maintenance of the KP feature export module)! This would mean you would just have to add your own file plugins/views_data_export_style_export_gff3.inc with the code to retrieve the parents and format the output and add a small array to hook views_data_export_styles (see code below :)) to register it.

To add the export to an existing view, edit the view (i.e.: the default feature view can be used) at your site/admin/build/views. Add a data export display (using the drop-down on the left). Under Basic settings change the Style to GFF3 (this should show up once you've registered the export type and added an empty class in the plugins/views_data_export_style_export_gff3.inc file. clear the cache 2X if it doesn't before panicking :)). Select any options (make sure to check the parent sort checkbox so that the exposed filtering in the parent view is used for the export). Then under Data Export Settings set the path of your export (something like path/to/original/view/gff3) and Attach to: (the original view page). Once you save, an icon using the picture you provided when registering the export will show up at the bottom on the original view. If you click it, it should download a file formatted using your plugin.

Hope that makes sense! Feel free to email me any questions :)
~Lacey

function chado_feature_export_views_data_export_styles ($style_defaults) {

  $style_defaults['path'] = drupal_get_path('module', 'chado_feature_export') . '/plugins';

  return array(
      'views_data_export_fasta' => array(
        'title' => t('FASTA'),
        'help' => t('Display the fasta records associated with a view.'),
        'handler' => 'views_data_export_plugin_style_export_fasta',
        'export headers' => array('Content-Type: text/plain'),
        'export feed type' => 'fasta',
        'export feed text' => 'FASTA',
        'export feed file' => '%view.fasta',
        'export feed icon' => drupal_get_path('module', 'chado_feature_export') . '/images/fasta.png',
      ) + $style_defaults,  

      'views_data_export_kaspar' => array(
        'title' => t('KASPar'),
        'help' => t('Display the marked up fasta records associated with a view.'),
        'handler' => 'views_data_export_plugin_style_export_kaspar',
        'export headers' => array('Content-Type: text/plain'),
        'export feed type' => 'kaspar',
        'export feed text' => 'KASPar',
        'export feed file' => '%view.fasta',
        'export feed icon' => drupal_get_path('module', 'chado_feature_export') . '/images/kaspar.png',
      ) + $style_defaults,  
      
      // YOU WOULD ADD THIS
      // Registers a GFF3 Export Style
      'views_data_export_gff3' => array(
        // information displayed when picking a data export style
        'title' => t('GFF3'),
        'help' => t('Display the GFF3 records associated with a view.'),
        // the name of the class containing the plugin code
        'handler' => 'views_data_export_plugin_style_export_gff3',
        'export headers' => array('Content-Type: text/plain'),
        'export feed type' => 'gff3',
        'export feed text' => 'GFF3',
        'export feed file' => '%view.gff3',
        // below is the path to the icon you want used for the feed
        // this will show up on the parent feature view and when clicked will begin the download
        'export feed icon' => drupal_get_path('module', 'chado_feature_export') . '/images/kaspar.png',
      ) + $style_defaults,
      // ADD UP TO HERE
  );
}

On 2013-07-25, at 11:59 AM, Scott Cain <[hidden email]> wrote:

Hi Eric,

I cc'ed both the Tripal mailing list (since this is where the discussion started) and the schema mailing list since it is a more general topic as well.

The tables in Chado that have gff in the name have to do with aspects of processing GFF as it's loaded and won't be of any use dumping GFF out.  There are a few views that would help though.  Specifically, I used the gff3view when writing the gff_string method of Bio::DB::Das::Chado::Segment::Feature, which I used for supporting GBrowse's GFF dumping functionality (at least, I'm pretty sure that's what I did; it was a long time ago).  That is a reasonable place to start.

Another thing you could look at is the bulkfiles functionality of GMODTools, which is distributed with the Chado installer.  It has a steeper learning curve (and I'm not the one who wrote the documentation :-), but once it's set up and configured it would probably be faster at generating things like GFF and fasta files on a whole-organism basis.

Scott



On Thu, Jul 25, 2013 at 1:26 PM, Eric Rasche <[hidden email]> wrote:
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi Scott,

Yes, absolutely via cached/pre-generated GFFs. I saw some GFF related
functions in the chado schema, is there anywhere I should start looking
for such functions when I go to write the download module?

Most of the artemis issue was that it required us to patch in SSL
support for database connections like Chado. That has now been submitted
as a merge request to Sanger.

Cheers,
Eric

On 07/25/2013 12:19 PM, Scott Cain wrote:
> Hi Eric,
>
> It makes a lot of sense to have a "download GFF" button on an organism's
> page, but I would think it would be better to have that has pre-generated
> GFF, since it could be quite a drain on the database's resources to
> generate a whole organism's GFF on the fly.
>
> I'm glad you got the Artemis stuff sorted out.
>
> Scott
>
>
>
> On Thu, Jul 25, 2013 at 1:07 PM, Eric Rasche <[hidden email]> wrote:
>
> Hi Scott,
>
> Well, this was posted a while ago, and since then I've managed to get
> Artemis to talk to Chado, which solves my problem in another manner.
>
> If GBrowse has an export option then that would have otherwise answered
> my question. We deployed a gbrowse instance, but haven't used it yet.
>
> What I had been imagining was simply a "Download GFF3" button on the
> organism pages, allowing for a one click download of that organism's
> file. However, since gbrowse does this, writing that feature again
> probably wouldn't be very useful.
>
>
> Cheers,
> Eric Rasche
>
> On 07/25/2013 12:02 PM, Scott Cain wrote:
>>>> Hi Eric,
>>>>
>>>> I'm not sure how generically useful that would be (though I can't speak
> for
>>>> the Tripal developers).  GBrowse has a GFF3 export option, and there are
>>>> command line tools as well.  What would you want in terms of a user
>>>> interface?
>>>>
>>>> Scott
>>>>
>>>>
>>>>
>>>> On Tue, Jul 23, 2013 at 12:09 PM, Eric Rasche <[hidden email]>
> wrote:
>>>>
>>>> Hello all,
>>>>
>>>>  Is there currently any plans for functionality to export a GFF3 file
>>>> from tripal?
>>>>
>>>> Since I'm having issues getting WebApollo to work with Chado, we'll
>>>> continue to be editing these genomes in Artemis.
>>>>
>>>> Cheers,
>>>> Eric
>>>>
>>>>
>>>>>
>>>>>
>>>>>
> ------------------------------------------------------------------------------
>>>>> See everything from the browser to the database with AppDynamics
>>>>> Get end-to-end visibility with application monitoring from AppDynamics
>>>>> Isolate bottlenecks and diagnose root cause in seconds.
>>>>> Start your free trial of AppDynamics Pro today!
>>>>>
> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk
>>>>> _______________________________________________
>>>>> Gmod-tripal mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>
>>>>
>>>>
>>>>
>>
>
>
>
- --
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843
<a href="tel:404-692-2048" value="+14046922048">404-692-2048
[hidden email]
[hidden email]
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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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Re: [Gmod-tripal] exporting GFF file

Stephen Ficklin-2
Hi Eric et al,

I have added a request to the Tripal Issues for a GFF3 exporter to be included in Tripal.  Eric, if you have a Drupal account you can follow that issue and when updates are posted to it you'll be notified.  Here's the link to the issue:

https://drupal.org/node/2052833

Stephen

On 7/25/2013 4:06 PM, Lacey-Anne Sanderson wrote:
Hi Eric,

If I were going to add exporting of GFF3 to Tripal I would create a new views bulk data export plugin like we did for exporting FASTA files. This would allow you to add a data export display to any feature view of style GFF3 which would give you a feed button exporting all the current features in the view (including exposed filtering :D) in GFF3 format. I would code this up myself if I weren't on maternity leave with my time dictated by a cute but very demanding boss :p

The advantages of this are:
 -  re-usability (it's generic enough for any Tripal website and can be used on multiple views in your own site with many different existing filters)
 -  allows you to export any set of features in a Tripal chado database by adding already existing filters to a feature view (i.e.: easy to say export all features in a given analysis/library or of a given type or from a given organism -including any combination of such options :))
 - requires minimal coding since the infrastructure is already there (the code to get the features to be exported, display filtering options to the user/admin, etc. is already done)
 - hooks into the views module allowing it to be used not just on feature views but also materialized views created through Tripal that can provide the necessary feature fields (allows you to do your own filtering using SQL if there are not the correct views filters yet making for the ultimate in flexibility)
  - probably many others I can't think of at this time :)

I would start by looking at how my marked-up FASTA export plugin was coded since it retrieves the parent features as well. It's contained in my KP Feature Export module (https://drupal.org/sandbox/laceysanderson/1341380). Specifically, you want to look at plugins/views_data_export_style_export_kaspar.inc. This file contains all the code needed to make the export style. Other then that you just need to register the export style in the .module file using hook views_data_export_styles (you can see an example in my module and I added code at the bottom of this email showing how you would add the registration to my own module).

I would love it if you submitted this export type as a patch to my module (I would of course give you recognition on the info page of the module :)) since it would be a Very useful export type to have (I would maintain it in the future as regular maintenance of the KP feature export module)! This would mean you would just have to add your own file plugins/views_data_export_style_export_gff3.inc with the code to retrieve the parents and format the output and add a small array to hook views_data_export_styles (see code below :)) to register it.

To add the export to an existing view, edit the view (i.e.: the default feature view can be used) at your site/admin/build/views. Add a data export display (using the drop-down on the left). Under Basic settings change the Style to GFF3 (this should show up once you've registered the export type and added an empty class in the plugins/views_data_export_style_export_gff3.inc file. clear the cache 2X if it doesn't before panicking :)). Select any options (make sure to check the parent sort checkbox so that the exposed filtering in the parent view is used for the export). Then under Data Export Settings set the path of your export (something like path/to/original/view/gff3) and Attach to: (the original view page). Once you save, an icon using the picture you provided when registering the export will show up at the bottom on the original view. If you click it, it should download a file formatted using your plugin.

Hope that makes sense! Feel free to email me any questions :)
~Lacey

function chado_feature_export_views_data_export_styles ($style_defaults) {

  $style_defaults['path'] = drupal_get_path('module', 'chado_feature_export') . '/plugins';

  return array(
      'views_data_export_fasta' => array(
        'title' => t('FASTA'),
        'help' => t('Display the fasta records associated with a view.'),
        'handler' => 'views_data_export_plugin_style_export_fasta',
        'export headers' => array('Content-Type: text/plain'),
        'export feed type' => 'fasta',
        'export feed text' => 'FASTA',
        'export feed file' => '%view.fasta',
        'export feed icon' => drupal_get_path('module', 'chado_feature_export') . '/images/fasta.png',
      ) + $style_defaults,  

      'views_data_export_kaspar' => array(
        'title' => t('KASPar'),
        'help' => t('Display the marked up fasta records associated with a view.'),
        'handler' => 'views_data_export_plugin_style_export_kaspar',
        'export headers' => array('Content-Type: text/plain'),
        'export feed type' => 'kaspar',
        'export feed text' => 'KASPar',
        'export feed file' => '%view.fasta',
        'export feed icon' => drupal_get_path('module', 'chado_feature_export') . '/images/kaspar.png',
      ) + $style_defaults,  
      
      // YOU WOULD ADD THIS
      // Registers a GFF3 Export Style
      'views_data_export_gff3' => array(
        // information displayed when picking a data export style
        'title' => t('GFF3'),
        'help' => t('Display the GFF3 records associated with a view.'),
        // the name of the class containing the plugin code
        'handler' => 'views_data_export_plugin_style_export_gff3',
        'export headers' => array('Content-Type: text/plain'),
        'export feed type' => 'gff3',
        'export feed text' => 'GFF3',
        'export feed file' => '%view.gff3',
        // below is the path to the icon you want used for the feed
        // this will show up on the parent feature view and when clicked will begin the download
        'export feed icon' => drupal_get_path('module', 'chado_feature_export') . '/images/kaspar.png',
      ) + $style_defaults,
      // ADD UP TO HERE
  );
}

On 2013-07-25, at 11:59 AM, Scott Cain <[hidden email]> wrote:

Hi Eric,

I cc'ed both the Tripal mailing list (since this is where the discussion started) and the schema mailing list since it is a more general topic as well.

The tables in Chado that have gff in the name have to do with aspects of processing GFF as it's loaded and won't be of any use dumping GFF out.  There are a few views that would help though.  Specifically, I used the gff3view when writing the gff_string method of Bio::DB::Das::Chado::Segment::Feature, which I used for supporting GBrowse's GFF dumping functionality (at least, I'm pretty sure that's what I did; it was a long time ago).  That is a reasonable place to start.

Another thing you could look at is the bulkfiles functionality of GMODTools, which is distributed with the Chado installer.  It has a steeper learning curve (and I'm not the one who wrote the documentation :-), but once it's set up and configured it would probably be faster at generating things like GFF and fasta files on a whole-organism basis.

Scott



On Thu, Jul 25, 2013 at 1:26 PM, Eric Rasche <[hidden email]> wrote:
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi Scott,

Yes, absolutely via cached/pre-generated GFFs. I saw some GFF related
functions in the chado schema, is there anywhere I should start looking
for such functions when I go to write the download module?

Most of the artemis issue was that it required us to patch in SSL
support for database connections like Chado. That has now been submitted
as a merge request to Sanger.

Cheers,
Eric

On 07/25/2013 12:19 PM, Scott Cain wrote:
> Hi Eric,
>
> It makes a lot of sense to have a "download GFF" button on an organism's
> page, but I would think it would be better to have that has pre-generated
> GFF, since it could be quite a drain on the database's resources to
> generate a whole organism's GFF on the fly.
>
> I'm glad you got the Artemis stuff sorted out.
>
> Scott
>
>
>
> On Thu, Jul 25, 2013 at 1:07 PM, Eric Rasche <[hidden email]> wrote:
>
> Hi Scott,
>
> Well, this was posted a while ago, and since then I've managed to get
> Artemis to talk to Chado, which solves my problem in another manner.
>
> If GBrowse has an export option then that would have otherwise answered
> my question. We deployed a gbrowse instance, but haven't used it yet.
>
> What I had been imagining was simply a "Download GFF3" button on the
> organism pages, allowing for a one click download of that organism's
> file. However, since gbrowse does this, writing that feature again
> probably wouldn't be very useful.
>
>
> Cheers,
> Eric Rasche
>
> On 07/25/2013 12:02 PM, Scott Cain wrote:
>>>> Hi Eric,
>>>>
>>>> I'm not sure how generically useful that would be (though I can't speak
> for
>>>> the Tripal developers).  GBrowse has a GFF3 export option, and there are
>>>> command line tools as well.  What would you want in terms of a user
>>>> interface?
>>>>
>>>> Scott
>>>>
>>>>
>>>>
>>>> On Tue, Jul 23, 2013 at 12:09 PM, Eric Rasche <[hidden email]>
> wrote:
>>>>
>>>> Hello all,
>>>>
>>>>  Is there currently any plans for functionality to export a GFF3 file
>>>> from tripal?
>>>>
>>>> Since I'm having issues getting WebApollo to work with Chado, we'll
>>>> continue to be editing these genomes in Artemis.
>>>>
>>>> Cheers,
>>>> Eric
>>>>
>>>>
>>>>>
>>>>>
>>>>>
> ------------------------------------------------------------------------------
>>>>> See everything from the browser to the database with AppDynamics
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>>>>>
>>>>
>>>>
>>>>
>>
>
>
>
- --
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843
<a moz-do-not-send="true" href="tel:404-692-2048" value="+14046922048">404-692-2048
[hidden email]
[hidden email]
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=fS68
-----END PGP SIGNATURE-----



--
------------------------------------------------------------------------
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: [Gmod-tripal] exporting GFF file

Eric Rasche
Hi Stephen,

Okay, I'll do that shortly. If this is free to take and work on, I'll be starting tomorrow.

Cheers,
Eric

Stephen Ficklin <[hidden email]> wrote:
Hi Eric et al,

I have added a request to the Tripal Issues for a GFF3 exporter to be included in Tripal.  Eric, if you have a Drupal account you can follow that issue and when updates are posted to it you'll be notified.  Here's the link to the issue:

https://drupal.org/node/2052833

Stephen

On 7/25/2013 4:06 PM, Lacey-Anne Sanderson wrote:
Hi Eric,

If I were going to add exporting of GFF3 to Tripal I would create a new views bulk data export plugin like we did for exporting FASTA files. This would allow you to add a data export display to any feature view of style GFF3 which would give you a feed button exporting all the current features in the view (including exposed filtering :D) in GFF3 format. I would code this up myself if I weren't on maternity leave with my time dictated by a cute but very demanding boss :p

The advantages of this are:
 -  re-usability (it's generic enough for any Tripal website and can be used on multiple views in your own site with many different existing filters)
 -  allows you to export any set of features in a Tripal chado database by adding already existing filters to a feature view (i.e.: easy to say export all features in a given analysis/library or of a given type or from a given organism -including any combination of such options :))
 - requires minimal coding since the infrastructure is already there (the code to get the features to be exported, display filtering options to the user/admin, etc. is already done)
 - hooks into the views module allowing it to be used not just on feature views but also materialized views created through Tripal that can provide the necessary feature fields (allows you to do your own filtering using SQL if there are not the correct views filters yet making for the ultimate in flexibility)
  - probably many others I can't think of at this time :)

I would start by looking at how my marked-up FASTA export plugin was coded since it retrieves the parent features as well. It's contained in my KP Feature Export module (https://drupal.org/sandbox/laceysanderson/1341380). Specifically, you want to look at plugins/views_data_export_style_export_kaspar.inc. This file contains all the code needed to make the export style. Other then that you just need to register the export style in the .module file using hook views_data_export_styles (you can see an example in my module and I added code at the bottom of this email showing how you would add the registration to my own module).

I would love it if you submitted this export type as a patch to my module (I would of course give you recognition on the info page of the module :)) since it would be a Very useful export type to have (I would maintain it in the future as regular maintenance of the KP feature export module)! This would mean you would just have to add your own file plugins/views_data_export_style_export_gff3.inc with the code to retrieve the parents and format the output and add a small array to hook views_data_export_styles (see code below :)) to register it.

To add the export to an existing view, edit the view (i.e.: the default feature view can be used) at your site/admin/build/views. Add a data export display (using the drop-down on the left). Under Basic settings change the Style to GFF3 (this should show up once you've registered the export type and added an empty class in the plugins/views_data_export_style_export_gff3.inc file. clear the cache 2X if it doesn't before panicking :)). Select any options (make sure to check the parent sort checkbox so that the exposed filtering in the parent view is used for the export). Then under Data Export Settings set the path of your export (something like path/to/original/view/gff3) and Attach to: (the original view page). Once you save, an icon using the picture you provided when registering the export will show up at the bottom on the original view. If you click it, it should download a file formatted using your plugin.

Hope that makes sense! Feel free to email me any questions :)
~Lacey

function chado_feature_export_views_data_export_styles ($style_defaults) {

  $style_defaults['path'] = drupal_get_path('module', 'chado_feature_export') . '/plugins';

  return array(
      'views_data_export_fasta' => array(
        'title' => t('FASTA'),
        'help' => t('Display the fasta records associated with a view.'),
        'handler' => 'views_data_export_plugin_style_export_fasta',
        'export headers' => array('Content-Type: text/plain'),
        'export feed type' => 'fasta',
        'export feed text' => 'FASTA',
        'export feed file' => '%view.fasta',
        'export feed icon' => drupal_get_path('module', 'chado_feature_export') . '/images/fasta.png',
      ) + $style_defaults,  

      'views_data_export_kaspar' => array(
        'title' => t('KASPar'),
        'help' => t('Display the marked up fasta records associated with a view.'),
        'handler' => 'views_data_export_plugin_style_export_kaspar',
        'export headers' => array('Content-Type: text/plain'),
        'export feed type' => 'kaspar',
        'export feed text' => 'KASPar',
        'export feed file' => '%view.fasta',
        'export feed icon' => drupal_get_path('module', 'chado_feature_export') . '/images/kaspar.png',
      ) + $style_defaults,  
      
      // YOU WOULD ADD THIS
      // Registers a GFF3 Export Style
      'views_data_export_gff3' => array(
        // information displayed when picking a data export style
        'title' => t('GFF3'),
        'help' => t('Display the GFF3 records associated with a view.'),
        // the name of the class containing the plugin code
        'handler' => 'views_data_export_plugin_style_export_gff3',
        'export headers' => array('Content-Type: text/plain'),
        'export feed type' => 'gff3',
        'export feed text' => 'GFF3',
        'export feed file' => '%view.gff3',
        // below is the path to the icon you want used for the feed
        // this will show up on the parent feature view and when clicked will begin the download
        'export feed icon' => drupal_get_path('module', 'chado_feature_export') . '/images/kaspar.png',
      ) + $style_defaults,
      // ADD UP TO HERE
  );
}

On 2013-07-25, at 11:59 AM, Scott Cain <[hidden email]> wrote:

Hi Eric,

I cc'ed both the Tripal mailing list (since this is where the discussion started) and the schema mailing list since it is a more general topic as well.

The tables in Chado that have gff in the name have to do with aspects of processing GFF as it's loaded and won't be of any use dumping GFF out.  There are a few views that would help though.  Specifically, I used the gff3view when writing the gff_string method of Bio::DB::Das::Chado::Segment::Feature, which I used for supporting GBrowse's GFF dumping functionality (at least, I'm pretty sure that's what I did; it was a long time ago).  That is a reasonable place to start.

Another thing you could look at is the bulkfiles functionality of GMODTools, which is distributed with the Chado installer.  It has a steeper learning curve (and I'm not the one who wrote the documentation :-), but once it's set up and configured it would probably be faster at generating things like GFF and fasta files on a whole-organism basis.

Scott



On Thu, Jul 25, 2013 at 1:26 PM, Eric Rasche <[hidden email]> wrote:
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi Scott,

Yes, absolutely via cached/pre-generated GFFs. I saw some GFF related
functions in the chado schema, is there anywhere I should start looking
for such functions when I go to write the download module?

Most of the artemis issue was that it required us to patch in SSL
support for database connections like Chado. That has now been submitted
as a merge request to Sanger.

Cheers,
Eric

On 07/25/2013 12:19 PM, Scott Cain wrote:
> Hi Eric,
>
> It makes a lot of sense to have a "download GFF" button on an organism's
> page, but I would think it would be better to have that has pre-generated
> GFF, since it could be quite a drain on the database's resources to
> generate a whole organism's GFF on the fly.
>
> I'm glad you got the Artemis stuff sorted out.
>
> Scott
>
>
>
> On Thu, Jul 25, 2013 at 1:07 PM, Eric Rasche <[hidden email]> wrote:
>
> Hi Scott,
>
> Well, this was posted a while ago, and since then I've managed to get
> Artemis to talk to Chado, which solves my problem in another manner.
>
> If GBrowse has an export option then that would have otherwise answered
> my question. We deployed a gbrowse instance, but haven't used it yet.
>
> What I had been imagining was simply a "Download GFF3" button on the
> organism pages, allowing for a one click download of that organism's
> file. However, since gbrowse does this, writing that feature again
> probably wouldn't be very useful.
>
>
> Cheers,
> Eric Rasche
>
> On 07/25/2013 12:02 PM, Scott Cain wrote:
>>>> Hi Eric,
>>>>
>>>> I'm not sure how generically useful that would be (though I can't speak
> for
>>>> the Tripal developers).  GBrowse has a GFF3 export option, and there are
>>>> command line tools as well.  What would you want in terms of a user
>>>> interface?
>>>>
>>>> Scott
>>>>
>>>>
>>>>
>>>> On Tue, Jul 23, 2013 at 12:09 PM, Eric Rasche <[hidden email]>
> wrote:
>>>>
>>>> Hello all,
>>>>
>>>>  Is there currently any plans for functionality to export a GFF3 file
>>>> from tripal?
>>>>
>>>> Since I'm having issues getting WebApollo to work with Chado, we'll
>>>> continue to be editing these genomes in Artemis.
>>>>
>>>> Cheers,
>>>> Eric
>>>>
>>>>
>>>>>
>>>>>
>>>>>
> ------------------------------------------------------------------------------
>>>>> See everything from the browser to the database with AppDynamics
>>>>> Get end-to-end visibility with application monitoring from AppDynamics
>>>>> Isolate bottlenecks and diagnose root cause in seconds.
>>>>> Start your free trial of AppDynamics Pro today!
>>>>>
> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk
>>>>> _______________________________________________
>>>>> Gmod-tripal mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>
>>>>
>>>>
>>>>
>>
>
>
>
- --
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843
<a moz-do-not-send="true" href="tel:404-692-2048" value="+14046922048">404-692-2048
[hidden email]
[hidden email]
-----BEGIN PGP SIGNATURE-----
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Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/

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=fS68
-----END PGP SIGNATURE-----



--
------------------------------------------------------------------------
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: [Gmod-tripal] exporting GFF file

Stephen Ficklin-2
Hi Eric,

Feel free to download and extend Tripal all you like.  You can obtain the most recent development branch by following the instructions on this page: http://tripal.info/node/63.  If you integrate with Lacey's module she can coordinate with you.  If you plan to start your own module feel free to subscribe to the developer's mailing list (https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel) and post questions, suggestions or progress if you like.   For reference, you may find the Tripal API documentation useful (http://tripal.info/sites/default/files/tripal_v1.1_api/index.html) and the Developer's Handbook (http://www.gmod.org/wiki/Tripal_Developer's_Handbook).

Stephen


On 7/29/2013 1:01 PM, Eric Rasche wrote:
Hi Stephen,

Okay, I'll do that shortly. If this is free to take and work on, I'll be starting tomorrow.

Cheers,
Eric

Stephen Ficklin [hidden email] wrote:
Hi Eric et al,

I have added a request to the Tripal Issues for a GFF3 exporter to be included in Tripal.  Eric, if you have a Drupal account you can follow that issue and when updates are posted to it you'll be notified.  Here's the link to the issue:

https://drupal.org/node/2052833

Stephen

On 7/25/2013 4:06 PM, Lacey-Anne Sanderson wrote:
Hi Eric,

If I were going to add exporting of GFF3 to Tripal I would create a new views bulk data export plugin like we did for exporting FASTA files. This would allow you to add a data export display to any feature view of style GFF3 which would give you a feed button exporting all the current features in the view (including exposed filtering :D) in GFF3 format. I would code this up myself if I weren't on maternity leave with my time dictated by a cute but very demanding boss :p

The advantages of this are:
 -  re-usability (it's generic enough for any Tripal website and can be used on multiple views in your own site with many different existing filters)
 -  allows you to export any set of features in a Tripal chado database by adding already existing filters to a feature view (i.e.: easy to say export all features in a given analysis/library or of a given type or from a given organism -including any combination of such options :))
 - requires minimal coding since the infrastructure is already there (the code to get the features to be exported, display filtering options to the user/admin, etc. is already done)
 - hooks into the views module allowing it to be used not just on feature views but also materialized views created through Tripal that can provide the necessary feature fields (allows you to do your own filtering using SQL if there are not the correct views filters yet making for the ultimate in flexibility)
  - probably many others I can't think of at this time :)

I would start by looking at how my marked-up FASTA export plugin was coded since it retrieves the parent features as well. It's contained in my KP Feature Export module (https://drupal.org/sandbox/laceysanderson/1341380). Specifically, you want to look at plugins/views_data_export_style_export_kaspar.inc. This file contains all the code needed to make the export style. Other then that you just need to register the export style in the .module file using hook views_data_export_styles (you can see an example in my module and I added code at the bottom of this email showing how you would add the registration to my own module).

I would love it if you submitted this export type as a patch to my module (I would of course give you recognition on the info page of the module :)) since it would be a Very useful export type to have (I would maintain it in the future as regular maintenance of the KP feature export module)! This would mean you would just have to add your own file plugins/views_data_export_style_export_gff3.inc with the code to retrieve the parents and format the output and add a small array to hook views_data_export_styles (see code below :)) to register it.

To add the export to an existing view, edit the view (i.e.: the default feature view can be used) at your site/admin/build/views. Add a data export display (using the drop-down on the left). Under Basic settings change the Style to GFF3 (this should show up once you've registered the export type and added an empty class in the plugins/views_data_export_style_export_gff3.inc file. clear the cache 2X if it doesn't before panicking :)). Select any options (make sure to check the parent sort checkbox so that the exposed filtering in the parent view is used for the export). Then under Data Export Settings set the path of your export (something like path/to/original/view/gff3) and Attach to: (the original view page). Once you save, an icon using the picture you provided when registering the export will show up at the bottom on the original view. If you click it, it should download a file formatted using your plugin.

Hope that makes sense! Feel free to email me any questions :)
~Lacey

function chado_feature_export_views_data_export_styles ($style_defaults) {

  $style_defaults['path'] = drupal_get_path('module', 'chado_feature_export') . '/plugins';

  return array(
      'views_data_export_fasta' => array(
        'title' => t('FASTA'),
        'help' => t('Display the fasta records associated with a view.'),
        'handler' => 'views_data_export_plugin_style_export_fasta',
        'export headers' => array('Content-Type: text/plain'),
        'export feed type' => 'fasta',
        'export feed text' => 'FASTA',
        'export feed file' => '%view.fasta',
        'export feed icon' => drupal_get_path('module', 'chado_feature_export') . '/images/fasta.png',
      ) + $style_defaults,  

      'views_data_export_kaspar' => array(
        'title' => t('KASPar'),
        'help' => t('Display the marked up fasta records associated with a view.'),
        'handler' => 'views_data_export_plugin_style_export_kaspar',
        'export headers' => array('Content-Type: text/plain'),
        'export feed type' => 'kaspar',
        'export feed text' => 'KASPar',
        'export feed file' => '%view.fasta',
        'export feed icon' => drupal_get_path('module', 'chado_feature_export') . '/images/kaspar.png',
      ) + $style_defaults,  
      
      // YOU WOULD ADD THIS
      // Registers a GFF3 Export Style
      'views_data_export_gff3' => array(
        // information displayed when picking a data export style
        'title' => t('GFF3'),
        'help' => t('Display the GFF3 records associated with a view.'),
        // the name of the class containing the plugin code
        'handler' => 'views_data_export_plugin_style_export_gff3',
        'export headers' => array('Content-Type: text/plain'),
        'export feed type' => 'gff3',
        'export feed text' => 'GFF3',
        'export feed file' => '%view.gff3',
        // below is the path to the icon you want used for the feed
        // this will show up on the parent feature view and when clicked will begin the download
        'export feed icon' => drupal_get_path('module', 'chado_feature_export') . '/images/kaspar.png',
      ) + $style_defaults,
      // ADD UP TO HERE
  );
}

On 2013-07-25, at 11:59 AM, Scott Cain <[hidden email]> wrote:

Hi Eric,

I cc'ed both the Tripal mailing list (since this is where the discussion started) and the schema mailing list since it is a more general topic as well.

The tables in Chado that have gff in the name have to do with aspects of processing GFF as it's loaded and won't be of any use dumping GFF out.  There are a few views that would help though.  Specifically, I used the gff3view when writing the gff_string method of Bio::DB::Das::Chado::Segment::Feature, which I used for supporting GBrowse's GFF dumping functionality (at least, I'm pretty sure that's what I did; it was a long time ago).  That is a reasonable place to start.

Another thing you could look at is the bulkfiles functionality of GMODTools, which is distributed with the Chado installer.  It has a steeper learning curve (and I'm not the one who wrote the documentation :-), but once it's set up and configured it would probably be faster at generating things like GFF and fasta files on a whole-organism basis.

Scott



On Thu, Jul 25, 2013 at 1:26 PM, Eric Rasche <[hidden email]> wrote:
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi Scott,

Yes, absolutely via cached/pre-generated GFFs. I saw some GFF related
functions in the chado schema, is there anywhere I should start looking
for such functions when I go to write the download module?

Most of the artemis issue was that it required us to patch in SSL
support for database connections like Chado. That has now been submitted
as a merge request to Sanger.

Cheers,
Eric

On 07/25/2013 12:19 PM, Scott Cain wrote:
> Hi Eric,
>
> It makes a lot of sense to have a "download GFF" button on an organism's
> page, but I would think it would be better to have that has pre-generated
> GFF, since it could be quite a drain on the database's resources to
> generate a whole organism's GFF on the fly.
>
> I'm glad you got the Artemis stuff sorted out.
>
> Scott
>
>
>
> On Thu, Jul 25, 2013 at 1:07 PM, Eric Rasche <[hidden email]> wrote:
>
> Hi Scott,
>
> Well, this was posted a while ago, and since then I've managed to get
> Artemis to talk to Chado, which solves my problem in another manner.
>
> If GBrowse has an export option then that would have otherwise answered
> my question. We deployed a gbrowse instance, but haven't used it yet.
>
> What I had been imagining was simply a "Download GFF3" button on the
> organism pages, allowing for a one click download of that organism's
> file. However, since gbrowse does this, writing that feature again
> probably wouldn't be very useful.
>
>
> Cheers,
> Eric Rasche
>
> On 07/25/2013 12:02 PM, Scott Cain wrote:
>>>> Hi Eric,
>>>>
>>>> I'm not sure how generically useful that would be (though I can't speak
> for
>>>> the Tripal developers).  GBrowse has a GFF3 export option, and there are
>>>> command line tools as well.  What would you want in terms of a user
>>>> interface?
>>>>
>>>> Scott
>>>>
>>>>
>>>>
>>>> On Tue, Jul 23, 2013 at 12:09 PM, Eric Rasche <[hidden email]>
> wrote:
>>>>
>>>> Hello all,
>>>>
>>>>  Is there currently any plans for functionality to export a GFF3 file
>>>> from tripal?
>>>>
>>>> Since I'm having issues getting WebApollo to work with Chado, we'll
>>>> continue to be editing these genomes in Artemis.
>>>>
>>>> Cheers,
>>>> Eric
>>>>
>>>>
>>>>>
>>>>>
>>>>>
> ------------------------------------------------------------------------------
>>>>> See everything from the browser to the database with AppDynamics
>>>>> Get end-to-end visibility with application monitoring from AppDynamics
>>>>> Isolate bottlenecks and diagnose root cause in seconds.
>>>>> Start your free trial of AppDynamics Pro today!
>>>>>
> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk
>>>>> _______________________________________________
>>>>> Gmod-tripal mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>
>>>>
>>>>
>>>>
>>
>
>
>
- --
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843
<a moz-do-not-send="true" href="tel:404-692-2048" value="+14046922048">404-692-2048
[hidden email]
[hidden email]
-----BEGIN PGP SIGNATURE-----
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Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/

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6sFbJsbFPC+J/Un21w4Q
=fS68
-----END PGP SIGNATURE-----



--
------------------------------------------------------------------------
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: [Gmod-tripal] exporting GFF file

adf_ncgr
In reply to this post by Scott Cain
Hi Scott-
picking up this somewhat aged thread, specifically with reference to your comments here about the
bulkfiles functionality of GMODTools:

Another thing you could look at is the bulkfiles functionality of GMODTools, which is distributed with the Chado installer.  It has a steeper learning curve (and I'm not the one who wrote the documentation :-), but once it's set up and configured it would probably be faster at generating things like GFF and fasta files on a whole-organism basis.

my group has been struggling a bit trying to work our way up the steep learning curve you mention, and are wondering whether
this is still the recommended method for generating fasta/gffs from chado databases (and are other groups actively using it)?
If so, would this list be the best place to find some help in understanding how this system is intended to work? FWIW, I think we may
have run into a couple of bugs (or perhaps under-documented features) in trying to use the script on our database so far and would
be happy to give some feedback to whomever appropriate if it's still the recommended approach for GFF/fasta/etc. export from chado.

thanks

Andrew Farmer
Legume Information System



On 7/25/13 11:59 AM, Scott Cain wrote:
Hi Eric,

I cc'ed both the Tripal mailing list (since this is where the discussion started) and the schema mailing list since it is a more general topic as well.

The tables in Chado that have gff in the name have to do with aspects of processing GFF as it's loaded and won't be of any use dumping GFF out.  There are a few views that would help though.  Specifically, I used the gff3view when writing the gff_string method of Bio::DB::Das::Chado::Segment::Feature, which I used for supporting GBrowse's GFF dumping functionality (at least, I'm pretty sure that's what I did; it was a long time ago).  That is a reasonable place to start.

Another thing you could look at is the bulkfiles functionality of GMODTools, which is distributed with the Chado installer.  It has a steeper learning curve (and I'm not the one who wrote the documentation :-), but once it's set up and configured it would probably be faster at generating things like GFF and fasta files on a whole-organism basis.

Scott



On Thu, Jul 25, 2013 at 1:26 PM, Eric Rasche <[hidden email]> wrote:
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi Scott,

Yes, absolutely via cached/pre-generated GFFs. I saw some GFF related
functions in the chado schema, is there anywhere I should start looking
for such functions when I go to write the download module?

Most of the artemis issue was that it required us to patch in SSL
support for database connections like Chado. That has now been submitted
as a merge request to Sanger.

Cheers,
Eric

On 07/25/2013 12:19 PM, Scott Cain wrote:
> Hi Eric,
>
> It makes a lot of sense to have a "download GFF" button on an organism's
> page, but I would think it would be better to have that has pre-generated
> GFF, since it could be quite a drain on the database's resources to
> generate a whole organism's GFF on the fly.
>
> I'm glad you got the Artemis stuff sorted out.
>
> Scott
>
>
>
> On Thu, Jul 25, 2013 at 1:07 PM, Eric Rasche <[hidden email]> wrote:
>
> Hi Scott,
>
> Well, this was posted a while ago, and since then I've managed to get
> Artemis to talk to Chado, which solves my problem in another manner.
>
> If GBrowse has an export option then that would have otherwise answered
> my question. We deployed a gbrowse instance, but haven't used it yet.
>
> What I had been imagining was simply a "Download GFF3" button on the
> organism pages, allowing for a one click download of that organism's
> file. However, since gbrowse does this, writing that feature again
> probably wouldn't be very useful.
>
>
> Cheers,
> Eric Rasche
>
> On 07/25/2013 12:02 PM, Scott Cain wrote:
>>>> Hi Eric,
>>>>
>>>> I'm not sure how generically useful that would be (though I can't speak
> for
>>>> the Tripal developers).  GBrowse has a GFF3 export option, and there are
>>>> command line tools as well.  What would you want in terms of a user
>>>> interface?
>>>>
>>>> Scott
>>>>
>>>>
>>>>
>>>> On Tue, Jul 23, 2013 at 12:09 PM, Eric Rasche <[hidden email]>
> wrote:
>>>>
>>>> Hello all,
>>>>
>>>>  Is there currently any plans for functionality to export a GFF3 file
>>>> from tripal?
>>>>
>>>> Since I'm having issues getting WebApollo to work with Chado, we'll
>>>> continue to be editing these genomes in Artemis.
>>>>
>>>> Cheers,
>>>> Eric
>>>>
>>>>
>>>>>
>>>>>
>>>>>
> ------------------------------------------------------------------------------
>>>>> See everything from the browser to the database with AppDynamics
>>>>> Get end-to-end visibility with application monitoring from AppDynamics
>>>>> Isolate bottlenecks and diagnose root cause in seconds.
>>>>> Start your free trial of AppDynamics Pro today!
>>>>>
> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk
>>>>> _______________________________________________
>>>>> Gmod-tripal mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>
>>>>
>>>>
>>>>
>>
>
>
>
- --
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843
<a moz-do-not-send="true" href="tel:404-692-2048" value="+14046922048">404-692-2048
[hidden email]
[hidden email]
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.11 (GNU/Linux)
Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/

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=fS68
-----END PGP SIGNATURE-----



--
------------------------------------------------------------------------
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: [Gmod-tripal] exporting GFF file

Stephen Ficklin-2
Hi Andrew,

Can you provide a bit of details how you would like the GFF "dumper" to work, say if we added one to Tripal?

Thanks,
Stephen

On 1/2/2014 2:10 PM, Andrew Farmer wrote:
Hi Scott-
picking up this somewhat aged thread, specifically with reference to your comments here about the
bulkfiles functionality of GMODTools:

Another thing you could look at is the bulkfiles functionality of GMODTools, which is distributed with the Chado installer.  It has a steeper learning curve (and I'm not the one who wrote the documentation :-), but once it's set up and configured it would probably be faster at generating things like GFF and fasta files on a whole-organism basis.

my group has been struggling a bit trying to work our way up the steep learning curve you mention, and are wondering whether
this is still the recommended method for generating fasta/gffs from chado databases (and are other groups actively using it)?
If so, would this list be the best place to find some help in understanding how this system is intended to work? FWIW, I think we may
have run into a couple of bugs (or perhaps under-documented features) in trying to use the script on our database so far and would
be happy to give some feedback to whomever appropriate if it's still the recommended approach for GFF/fasta/etc. export from chado.

thanks

Andrew Farmer
Legume Information System



On 7/25/13 11:59 AM, Scott Cain wrote:
Hi Eric,

I cc'ed both the Tripal mailing list (since this is where the discussion started) and the schema mailing list since it is a more general topic as well.

The tables in Chado that have gff in the name have to do with aspects of processing GFF as it's loaded and won't be of any use dumping GFF out.  There are a few views that would help though.  Specifically, I used the gff3view when writing the gff_string method of Bio::DB::Das::Chado::Segment::Feature, which I used for supporting GBrowse's GFF dumping functionality (at least, I'm pretty sure that's what I did; it was a long time ago).  That is a reasonable place to start.

Another thing you could look at is the bulkfiles functionality of GMODTools, which is distributed with the Chado installer.  It has a steeper learning curve (and I'm not the one who wrote the documentation :-), but once it's set up and configured it would probably be faster at generating things like GFF and fasta files on a whole-organism basis.

Scott



On Thu, Jul 25, 2013 at 1:26 PM, Eric Rasche <[hidden email]> wrote:
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi Scott,

Yes, absolutely via cached/pre-generated GFFs. I saw some GFF related
functions in the chado schema, is there anywhere I should start looking
for such functions when I go to write the download module?

Most of the artemis issue was that it required us to patch in SSL
support for database connections like Chado. That has now been submitted
as a merge request to Sanger.

Cheers,
Eric

On 07/25/2013 12:19 PM, Scott Cain wrote:
> Hi Eric,
>
> It makes a lot of sense to have a "download GFF" button on an organism's
> page, but I would think it would be better to have that has pre-generated
> GFF, since it could be quite a drain on the database's resources to
> generate a whole organism's GFF on the fly.
>
> I'm glad you got the Artemis stuff sorted out.
>
> Scott
>
>
>
> On Thu, Jul 25, 2013 at 1:07 PM, Eric Rasche <[hidden email]> wrote:
>
> Hi Scott,
>
> Well, this was posted a while ago, and since then I've managed to get
> Artemis to talk to Chado, which solves my problem in another manner.
>
> If GBrowse has an export option then that would have otherwise answered
> my question. We deployed a gbrowse instance, but haven't used it yet.
>
> What I had been imagining was simply a "Download GFF3" button on the
> organism pages, allowing for a one click download of that organism's
> file. However, since gbrowse does this, writing that feature again
> probably wouldn't be very useful.
>
>
> Cheers,
> Eric Rasche
>
> On 07/25/2013 12:02 PM, Scott Cain wrote:
>>>> Hi Eric,
>>>>
>>>> I'm not sure how generically useful that would be (though I can't speak
> for
>>>> the Tripal developers).  GBrowse has a GFF3 export option, and there are
>>>> command line tools as well.  What would you want in terms of a user
>>>> interface?
>>>>
>>>> Scott
>>>>
>>>>
>>>>
>>>> On Tue, Jul 23, 2013 at 12:09 PM, Eric Rasche <[hidden email]>
> wrote:
>>>>
>>>> Hello all,
>>>>
>>>>  Is there currently any plans for functionality to export a GFF3 file
>>>> from tripal?
>>>>
>>>> Since I'm having issues getting WebApollo to work with Chado, we'll
>>>> continue to be editing these genomes in Artemis.
>>>>
>>>> Cheers,
>>>> Eric
>>>>
>>>>
>>>>>
>>>>>
>>>>>
> ------------------------------------------------------------------------------
>>>>> See everything from the browser to the database with AppDynamics
>>>>> Get end-to-end visibility with application monitoring from AppDynamics
>>>>> Isolate bottlenecks and diagnose root cause in seconds.
>>>>> Start your free trial of AppDynamics Pro today!
>>>>>
> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk
>>>>> _______________________________________________
>>>>> Gmod-tripal mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>
>>>>
>>>>
>>>>
>>
>
>
>
- --
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843
<a moz-do-not-send="true" href="tel:404-692-2048" value="+14046922048">404-692-2048
[hidden email]
[hidden email]
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Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/

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Ontario Institute for Cancer Research


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Re: [Gmod-tripal] exporting GFF file

adf_ncgr
Hi Stephen-
well, to be honest, I was hoping that the existing GFF dumper given by the gmod_bulkfiles.pl script
would represent a "gold standard" for representing chado content in GFF3 format and that I wouldn't
have to think too much about how I would like it to work ;) Is there a compelling reason to consider
reimplementing such a function from scratch in the context of Tripal rather than trying to harness the
existing logic of the gmod_bulkfiles.pl script (assuming it is still supported)? This may be a naive question-
I have to admit to copious confusion at what exists in the chado ecosystem...

thanks!

Andrew



On 1/2/14 12:17 PM, Stephen Ficklin wrote:
Hi Andrew,

Can you provide a bit of details how you would like the GFF "dumper" to work, say if we added one to Tripal?

Thanks,
Stephen

On 1/2/2014 2:10 PM, Andrew Farmer wrote:
Hi Scott-
picking up this somewhat aged thread, specifically with reference to your comments here about the
bulkfiles functionality of GMODTools:

Another thing you could look at is the bulkfiles functionality of GMODTools, which is distributed with the Chado installer.  It has a steeper learning curve (and I'm not the one who wrote the documentation :-), but once it's set up and configured it would probably be faster at generating things like GFF and fasta files on a whole-organism basis.

my group has been struggling a bit trying to work our way up the steep learning curve you mention, and are wondering whether
this is still the recommended method for generating fasta/gffs from chado databases (and are other groups actively using it)?
If so, would this list be the best place to find some help in understanding how this system is intended to work? FWIW, I think we may
have run into a couple of bugs (or perhaps under-documented features) in trying to use the script on our database so far and would
be happy to give some feedback to whomever appropriate if it's still the recommended approach for GFF/fasta/etc. export from chado.

thanks

Andrew Farmer
Legume Information System



On 7/25/13 11:59 AM, Scott Cain wrote:
Hi Eric,

I cc'ed both the Tripal mailing list (since this is where the discussion started) and the schema mailing list since it is a more general topic as well.

The tables in Chado that have gff in the name have to do with aspects of processing GFF as it's loaded and won't be of any use dumping GFF out.  There are a few views that would help though.  Specifically, I used the gff3view when writing the gff_string method of Bio::DB::Das::Chado::Segment::Feature, which I used for supporting GBrowse's GFF dumping functionality (at least, I'm pretty sure that's what I did; it was a long time ago).  That is a reasonable place to start.

Another thing you could look at is the bulkfiles functionality of GMODTools, which is distributed with the Chado installer.  It has a steeper learning curve (and I'm not the one who wrote the documentation :-), but once it's set up and configured it would probably be faster at generating things like GFF and fasta files on a whole-organism basis.

Scott



On Thu, Jul 25, 2013 at 1:26 PM, Eric Rasche <[hidden email]> wrote:
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi Scott,

Yes, absolutely via cached/pre-generated GFFs. I saw some GFF related
functions in the chado schema, is there anywhere I should start looking
for such functions when I go to write the download module?

Most of the artemis issue was that it required us to patch in SSL
support for database connections like Chado. That has now been submitted
as a merge request to Sanger.

Cheers,
Eric

On 07/25/2013 12:19 PM, Scott Cain wrote:
> Hi Eric,
>
> It makes a lot of sense to have a "download GFF" button on an organism's
> page, but I would think it would be better to have that has pre-generated
> GFF, since it could be quite a drain on the database's resources to
> generate a whole organism's GFF on the fly.
>
> I'm glad you got the Artemis stuff sorted out.
>
> Scott
>
>
>
> On Thu, Jul 25, 2013 at 1:07 PM, Eric Rasche <[hidden email]> wrote:
>
> Hi Scott,
>
> Well, this was posted a while ago, and since then I've managed to get
> Artemis to talk to Chado, which solves my problem in another manner.
>
> If GBrowse has an export option then that would have otherwise answered
> my question. We deployed a gbrowse instance, but haven't used it yet.
>
> What I had been imagining was simply a "Download GFF3" button on the
> organism pages, allowing for a one click download of that organism's
> file. However, since gbrowse does this, writing that feature again
> probably wouldn't be very useful.
>
>
> Cheers,
> Eric Rasche
>
> On 07/25/2013 12:02 PM, Scott Cain wrote:
>>>> Hi Eric,
>>>>
>>>> I'm not sure how generically useful that would be (though I can't speak
> for
>>>> the Tripal developers).  GBrowse has a GFF3 export option, and there are
>>>> command line tools as well.  What would you want in terms of a user
>>>> interface?
>>>>
>>>> Scott
>>>>
>>>>
>>>>
>>>> On Tue, Jul 23, 2013 at 12:09 PM, Eric Rasche <[hidden email]>
> wrote:
>>>>
>>>> Hello all,
>>>>
>>>>  Is there currently any plans for functionality to export a GFF3 file
>>>> from tripal?
>>>>
>>>> Since I'm having issues getting WebApollo to work with Chado, we'll
>>>> continue to be editing these genomes in Artemis.
>>>>
>>>> Cheers,
>>>> Eric
>>>>
>>>>
>>>>>
>>>>>
>>>>>
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>>>>
>>>>
>>
>
>
>
- --
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843
<a moz-do-not-send="true" href="tel:404-692-2048" value="+14046922048">404-692-2048
[hidden email]
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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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