[Gmod-ajax] display notes from GFF3

classic Classic list List threaded Threaded
8 messages Options
Reply | Threaded
Open this post in threaded view
|

[Gmod-ajax] display notes from GFF3

David Breimann
Hi Guys,

I use GFF3 files to load features to JBrowse. The last column in my GFF3 contains some free text notes ("Note=..."), as desctibed in the GFF3 specifications (http://www.sequenceontology.org/gff3.shtml). Can I make these notes visible when clicking (or better yet, hovering) on a feature in JBrowse?

Thanks,
Dave

------------------------------------------------------------------------------
This SF.net email is sponsored by

Make an app they can't live without
Enter the BlackBerry Developer Challenge
http://p.sf.net/sfu/RIM-dev2dev 
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
Reply | Threaded
Open this post in threaded view
|

Re: display notes from GFF3

Mitch Skinner
Making this nicer is definitely on the to-do list.  The best you can do right now is incorporate the note information into the label using a label callback, like we talked about last month:

http://gmod.827538.n3.nabble.com/Gmod-ajax-How-can-I-display-each-feature-name-tag-id-description-next-to-it-tp938564p938890.html

In the label callback, you should be able to get the "Note" field from the feature object using ->attributes("Note")

Mitch

On 08/09/2010 11:29 PM, David Breimann wrote:
Hi Guys,

I use GFF3 files to load features to JBrowse. The last column in my GFF3 contains some free text notes ("Note=..."), as desctibed in the GFF3 specifications (http://www.sequenceontology.org/gff3.shtml). Can I make these notes visible when clicking (or better yet, hovering) on a feature in JBrowse?

Thanks,
Dave
------------------------------------------------------------------------------ This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev
_______________________________________________ Gmod-ajax mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-ajax


------------------------------------------------------------------------------
This SF.net email is sponsored by

Make an app they can't live without
Enter the BlackBerry Developer Challenge
http://p.sf.net/sfu/RIM-dev2dev 
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
Reply | Threaded
Open this post in threaded view
|

Re: display notes from GFF3

David Breimann
Thank Mitch,
But can I do it using the command line attributes of flatfile-to-json.pl or do I have to use a config file?

On Wed, Aug 11, 2010 at 9:15 AM, Mitch Skinner <[hidden email]> wrote:
Making this nicer is definitely on the to-do list.  The best you can do right now is incorporate the note information into the label using a label callback, like we talked about last month:

http://gmod.827538.n3.nabble.com/Gmod-ajax-How-can-I-display-each-feature-name-tag-id-description-next-to-it-tp938564p938890.html

In the label callback, you should be able to get the "Note" field from the feature object using ->attributes("Note")

Mitch


On 08/09/2010 11:29 PM, David Breimann wrote:
Hi Guys,

I use GFF3 files to load features to JBrowse. The last column in my GFF3 contains some free text notes ("Note=..."), as desctibed in the GFF3 specifications (http://www.sequenceontology.org/gff3.shtml). Can I make these notes visible when clicking (or better yet, hovering) on a feature in JBrowse?

Thanks,
Dave
------------------------------------------------------------------------------ This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev
_______________________________________________ Gmod-ajax mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------------
This SF.net email is sponsored by

Make an app they can't live without
Enter the BlackBerry Developer Challenge
http://p.sf.net/sfu/RIM-dev2dev 
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
Reply | Threaded
Open this post in threaded view
|

Re: display notes from GFF3

Mitch Skinner
It's currently only implemented for use with a config file and biodb-to-json.pl.

The flatfile-to-json.pl command lines are so hugely complicated that I didn't expect that people would want to write perl callbacks and JSON snippets and so on as command line arguments.  The shell quote removal alone is a pain in the rear.  The whole point of the config file is to have a convenient way to specify all those settings in a simpler way.  And you can use the same input flat files with a config file and biodb-to-json.pl; the docs/tutorial/conf_files/volvox.json has an example.

Since people seem to want to use flatfile-to-json.pl so much, though, we'll probably try to bring them to parity in the future, but it's not yet implemented.

Mitch

On 08/10/2010 11:24 PM, David Breimann wrote:
Thank Mitch,
But can I do it using the command line attributes of flatfile-to-json.pl or do I have to use a config file?

On Wed, Aug 11, 2010 at 9:15 AM, Mitch Skinner <[hidden email]> wrote:
Making this nicer is definitely on the to-do list.  The best you can do right now is incorporate the note information into the label using a label callback, like we talked about last month:

http://gmod.827538.n3.nabble.com/Gmod-ajax-How-can-I-display-each-feature-name-tag-id-description-next-to-it-tp938564p938890.html

In the label callback, you should be able to get the "Note" field from the feature object using ->attributes("Note")

Mitch


On 08/09/2010 11:29 PM, David Breimann wrote:
Hi Guys,

I use GFF3 files to load features to JBrowse. The last column in my GFF3 contains some free text notes ("Note=..."), as desctibed in the GFF3 specifications (http://www.sequenceontology.org/gff3.shtml). Can I make these notes visible when clicking (or better yet, hovering) on a feature in JBrowse?

Thanks,
Dave
------------------------------------------------------------------------------ This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev
_______________________________________________ Gmod-ajax mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-ajax




------------------------------------------------------------------------------
This SF.net email is sponsored by

Make an app they can't live without
Enter the BlackBerry Developer Challenge
http://p.sf.net/sfu/RIM-dev2dev 
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
Reply | Threaded
Open this post in threaded view
|

Re: display notes from GFF3

David Breimann
I never fully got the idea of biodb-to-json.pl when I don't really have a db, just a flat file. Could you please point me to the biodb-to-json.pl equivalent of the simplest flatfile-to-json.pl example (e.g. loading "gene"s from a GFF3 file)?
I don't understand where does the filename goes.

On Wed, Aug 11, 2010 at 5:20 PM, Mitch Skinner <[hidden email]> wrote:
It's currently only implemented for use with a config file and biodb-to-json.pl.

The flatfile-to-json.pl command lines are so hugely complicated that I didn't expect that people would want to write perl callbacks and JSON snippets and so on as command line arguments.  The shell quote removal alone is a pain in the rear.  The whole point of the config file is to have a convenient way to specify all those settings in a simpler way.  And you can use the same input flat files with a config file and biodb-to-json.pl; the docs/tutorial/conf_files/volvox.json has an example.

Since people seem to want to use flatfile-to-json.pl so much, though, we'll probably try to bring them to parity in the future, but it's not yet implemented.

Mitch


On 08/10/2010 11:24 PM, David Breimann wrote:
Thank Mitch,
But can I do it using the command line attributes of flatfile-to-json.pl or do I have to use a config file?

On Wed, Aug 11, 2010 at 9:15 AM, Mitch Skinner <[hidden email]> wrote:
Making this nicer is definitely on the to-do list.  The best you can do right now is incorporate the note information into the label using a label callback, like we talked about last month:

http://gmod.827538.n3.nabble.com/Gmod-ajax-How-can-I-display-each-feature-name-tag-id-description-next-to-it-tp938564p938890.html

In the label callback, you should be able to get the "Note" field from the feature object using ->attributes("Note")

Mitch


On 08/09/2010 11:29 PM, David Breimann wrote:
Hi Guys,

I use GFF3 files to load features to JBrowse. The last column in my GFF3 contains some free text notes ("Note=..."), as desctibed in the GFF3 specifications (http://www.sequenceontology.org/gff3.shtml). Can I make these notes visible when clicking (or better yet, hovering) on a feature in JBrowse?

Thanks,
Dave
------------------------------------------------------------------------------ This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev
_______________________________________________ Gmod-ajax mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-ajax





------------------------------------------------------------------------------
This SF.net email is sponsored by

Make an app they can't live without
Enter the BlackBerry Developer Challenge
http://p.sf.net/sfu/RIM-dev2dev 
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
Reply | Threaded
Open this post in threaded view
|

Re: display notes from GFF3

Ian Holmes
David

The file that Mitch mentioned, docs/tutorial/conf_files/volvox.json ,
has an example of how to use a flatfile with biodb-to-json.pl

Ian

David Breimann wrote:

> I never fully got the idea of biodb-to-json.pl
> <http://biodb-to-json.pl/> when I don't really have a db, just a flat
> file. Could you please point me to the biodb-to-json.pl
> <http://biodb-to-json.pl/> equivalent of the simplest
> flatfile-to-json.pl <http://flatfile-to-json.pl/> example (e.g. loading
> "gene"s from a GFF3 file)?
> I don't understand where does the filename goes.
>
> On Wed, Aug 11, 2010 at 5:20 PM, Mitch Skinner
> <[hidden email] <mailto:[hidden email]>> wrote:
>
>     It's currently only implemented for use with a config file and
>     biodb-to-json.pl <http://biodb-to-json.pl>.
>
>     The flatfile-to-json.pl <http://flatfile-to-json.pl> command lines
>     are so hugely complicated that I didn't expect that people would
>     want to write perl callbacks and JSON snippets and so on as command
>     line arguments.  The shell quote removal alone is a pain in the
>     rear.  The whole point of the config file is to have a convenient
>     way to specify all those settings in a simpler way.  And you can use
>     the same input flat files with a config file and biodb-to-json.pl
>     <http://biodb-to-json.pl>; the docs/tutorial/conf_files/volvox.json
>     has an example.
>
>     Since people seem to want to use flatfile-to-json.pl
>     <http://flatfile-to-json.pl> so much, though, we'll probably try to
>     bring them to parity in the future, but it's not yet implemented.
>
>     Mitch
>
>
>     On 08/10/2010 11:24 PM, David Breimann wrote:
>>     Thank Mitch,
>>     But can I do it using the command line attributes of
>>     flatfile-to-json.pl <http://flatfile-to-json.pl> or do I have to
>>     use a config file?
>>
>>     On Wed, Aug 11, 2010 at 9:15 AM, Mitch Skinner
>>     <[hidden email] <mailto:[hidden email]>>
>>     wrote:
>>
>>         Making this nicer is definitely on the to-do list.  The best
>>         you can do right now is incorporate the note information into
>>         the label using a label callback, like we talked about last month:
>>
>>         http://gmod.827538.n3.nabble.com/Gmod-ajax-How-can-I-display-each-feature-name-tag-id-description-next-to-it-tp938564p938890.html
>>
>>         In the label callback, you should be able to get the "Note"
>>         field from the feature object using ->attributes("Note")
>>
>>         Mitch
>>
>>
>>         On 08/09/2010 11:29 PM, David Breimann wrote:
>>>         Hi Guys,
>>>
>>>         I use GFF3 files to load features to JBrowse. The last column
>>>         in my GFF3 contains some free text notes ("Note=..."), as
>>>         desctibed in the GFF3 specifications
>>>         (http://www.sequenceontology.org/gff3.shtml). Can I make
>>>         these notes visible when clicking (or better yet, hovering)
>>>         on a feature in JBrowse?
>>>
>>>         Thanks,
>>>         Dave
>>>
>>>
>>>         ------------------------------------------------------------------------------
>>>         This SF.net email is sponsored by
>>>
>>>         Make an app they can't live without
>>>         Enter the BlackBerry Developer Challenge
>>>         http://p.sf.net/sfu/RIM-dev2dev 
>>>
>>>
>>>         _______________________________________________
>>>         Gmod-ajax mailing list
>>>         [hidden email] <mailto:[hidden email]>
>>>         https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>>
>
>
>
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by
>
> Make an app they can't live without
> Enter the BlackBerry Developer Challenge
> http://p.sf.net/sfu/RIM-dev2dev 
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

------------------------------------------------------------------------------
This SF.net email is sponsored by

Make an app they can't live without
Enter the BlackBerry Developer Challenge
http://p.sf.net/sfu/RIM-dev2dev 
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
Reply | Threaded
Open this post in threaded view
|

Re: display notes from GFF3

Ian Holmes
 >> I don't understand where does the filename goes.

The JBrowse example uses a directory name rather than a single filename;
in this case the directory is scanned for all *.gff and *.gff3 files
(and compressed equivalents *.gff3.gz, *.gff3.bz2, etc). However I
believe you can also use a single filename if you prefer:

http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/DB/SeqFeature/Store/memory.pm


Best wishes
Ian

> David
>
> The file that Mitch mentioned, docs/tutorial/conf_files/volvox.json ,
> has an example of how to use a flatfile with biodb-to-json.pl
>
> Ian
>
> David Breimann wrote:
>> I never fully got the idea of biodb-to-json.pl
>> <http://biodb-to-json.pl/> when I don't really have a db, just a flat
>> file. Could you please point me to the biodb-to-json.pl
>> <http://biodb-to-json.pl/> equivalent of the simplest
>> flatfile-to-json.pl <http://flatfile-to-json.pl/> example (e.g. loading
>> "gene"s from a GFF3 file)?
>> I don't understand where does the filename goes.
>>
>> On Wed, Aug 11, 2010 at 5:20 PM, Mitch Skinner
>> <[hidden email] <mailto:[hidden email]>> wrote:
>>
>>     It's currently only implemented for use with a config file and
>>     biodb-to-json.pl <http://biodb-to-json.pl>.
>>
>>     The flatfile-to-json.pl <http://flatfile-to-json.pl> command lines
>>     are so hugely complicated that I didn't expect that people would
>>     want to write perl callbacks and JSON snippets and so on as command
>>     line arguments.  The shell quote removal alone is a pain in the
>>     rear.  The whole point of the config file is to have a convenient
>>     way to specify all those settings in a simpler way.  And you can use
>>     the same input flat files with a config file and biodb-to-json.pl
>>     <http://biodb-to-json.pl>; the docs/tutorial/conf_files/volvox.json
>>     has an example.
>>
>>     Since people seem to want to use flatfile-to-json.pl
>>     <http://flatfile-to-json.pl> so much, though, we'll probably try to
>>     bring them to parity in the future, but it's not yet implemented.
>>
>>     Mitch
>>
>>
>>     On 08/10/2010 11:24 PM, David Breimann wrote:
>>>     Thank Mitch,
>>>     But can I do it using the command line attributes of
>>>     flatfile-to-json.pl <http://flatfile-to-json.pl> or do I have to
>>>     use a config file?
>>>
>>>     On Wed, Aug 11, 2010 at 9:15 AM, Mitch Skinner
>>>     <[hidden email] <mailto:[hidden email]>>
>>>     wrote:
>>>
>>>         Making this nicer is definitely on the to-do list.  The best
>>>         you can do right now is incorporate the note information into
>>>         the label using a label callback, like we talked about last month:
>>>
>>>         http://gmod.827538.n3.nabble.com/Gmod-ajax-How-can-I-display-each-feature-name-tag-id-description-next-to-it-tp938564p938890.html
>>>
>>>         In the label callback, you should be able to get the "Note"
>>>         field from the feature object using ->attributes("Note")
>>>
>>>         Mitch
>>>
>>>
>>>         On 08/09/2010 11:29 PM, David Breimann wrote:
>>>>         Hi Guys,
>>>>
>>>>         I use GFF3 files to load features to JBrowse. The last column
>>>>         in my GFF3 contains some free text notes ("Note=..."), as
>>>>         desctibed in the GFF3 specifications
>>>>         (http://www.sequenceontology.org/gff3.shtml). Can I make
>>>>         these notes visible when clicking (or better yet, hovering)
>>>>         on a feature in JBrowse?
>>>>
>>>>         Thanks,
>>>>         Dave
>>>>
>>>>
>>>>         ------------------------------------------------------------------------------
>>>>         This SF.net email is sponsored by
>>>>
>>>>         Make an app they can't live without
>>>>         Enter the BlackBerry Developer Challenge
>>>>         http://p.sf.net/sfu/RIM-dev2dev 
>>>>
>>>>
>>>>         _______________________________________________
>>>>         Gmod-ajax mailing list
>>>>         [hidden email] <mailto:[hidden email]>
>>>>         https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
>>
>> ------------------------------------------------------------------------
>>
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by
>>
>> Make an app they can't live without
>> Enter the BlackBerry Developer Challenge
>> http://p.sf.net/sfu/RIM-dev2dev 
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by
>
> Make an app they can't live without
> Enter the BlackBerry Developer Challenge
> http://p.sf.net/sfu/RIM-dev2dev 
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

------------------------------------------------------------------------------
This SF.net email is sponsored by

Make an app they can't live without
Enter the BlackBerry Developer Challenge
http://p.sf.net/sfu/RIM-dev2dev 
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
Reply | Threaded
Open this post in threaded view
|

Re: display notes from GFF3

Ian Holmes
No, currently the wig-to-json script is the only way to do that.



On Aug 15, 2010, at 12:09 AM, David Breimann <[hidden email]> wrote:

Thanks. Can I also add wig files using config file?

On Wed, Aug 11, 2010 at 7:52 PM, Ian Holmes <[hidden email]> wrote:
>> I don't understand where does the filename goes.

The JBrowse example uses a directory name rather than a single filename; in this case the directory is scanned for all *.gff and *.gff3 files (and compressed equivalents *.gff3.gz, *.gff3.bz2, etc). However I believe you can also use a single filename if you prefer:

http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/DB/SeqFeature/Store/memory.pm


Best wishes
Ian


David

The file that Mitch mentioned, docs/tutorial/conf_files/volvox.json , has an example of how to use a flatfile with biodb-to-json.pl

Ian

David Breimann wrote:
I never fully got the idea of biodb-to-json.pl <http://biodb-to-json.pl/> when I don't really have a db, just a flat file. Could you please point me to the biodb-to-json.pl <http://biodb-to-json.pl/> equivalent of the simplest flatfile-to-json.pl <http://flatfile-to-json.pl/> example (e.g. loading "gene"s from a GFF3 file)?
I don't understand where does the filename goes.

On Wed, Aug 11, 2010 at 5:20 PM, Mitch Skinner <[hidden email] <mailto:[hidden email]>> wrote:

   It's currently only implemented for use with a config file and
   biodb-to-json.pl <http://biodb-to-json.pl>.

   The flatfile-to-json.pl <http://flatfile-to-json.pl> command lines
   are so hugely complicated that I didn't expect that people would
   want to write perl callbacks and JSON snippets and so on as command
   line arguments.  The shell quote removal alone is a pain in the
   rear.  The whole point of the config file is to have a convenient
   way to specify all those settings in a simpler way.  And you can use
   the same input flat files with a config file and biodb-to-json.pl
   <http://biodb-to-json.pl>; the docs/tutorial/conf_files/volvox.json
   has an example.

   Since people seem to want to use flatfile-to-json.pl
   <http://flatfile-to-json.pl> so much, though, we'll probably try to
   bring them to parity in the future, but it's not yet implemented.

   Mitch


   On 08/10/2010 11:24 PM, David Breimann wrote:
   Thank Mitch,
   But can I do it using the command line attributes of
   flatfile-to-json.pl <http://flatfile-to-json.pl> or do I have to
   use a config file?

   On Wed, Aug 11, 2010 at 9:15 AM, Mitch Skinner
   <[hidden email] <mailto:[hidden email]>>
   wrote:

       Making this nicer is definitely on the to-do list.  The best
       you can do right now is incorporate the note information into
       the label using a label callback, like we talked about last month:

       http://gmod.827538.n3.nabble.com/Gmod-ajax-How-can-I-display-each-feature-name-tag-id-description-next-to-it-tp938564p938890.html

       In the label callback, you should be able to get the "Note"
       field from the feature object using ->attributes("Note")

       Mitch


       On 08/09/2010 11:29 PM, David Breimann wrote:
       Hi Guys,

       I use GFF3 files to load features to JBrowse. The last column
       in my GFF3 contains some free text notes ("Note=..."), as
       desctibed in the GFF3 specifications
       (http://www.sequenceontology.org/gff3.shtml). Can I make
       these notes visible when clicking (or better yet, hovering)
       on a feature in JBrowse?

       Thanks,
       Dave


       ------------------------------------------------------------------------------
       This SF.net email is sponsored by
       Make an app they can't live without
       Enter the BlackBerry Developer Challenge
       http://p.sf.net/sfu/RIM-dev2dev

       _______________________________________________
       Gmod-ajax mailing list
       [hidden email] <mailto:[hidden email]>
       https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------

------------------------------------------------------------------------------
This SF.net email is sponsored by
Make an app they can't live without
Enter the BlackBerry Developer Challenge
http://p.sf.net/sfu/RIM-dev2dev

------------------------------------------------------------------------

_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

------------------------------------------------------------------------------
This SF.net email is sponsored by
Make an app they can't live without
Enter the BlackBerry Developer Challenge
http://p.sf.net/sfu/RIM-dev2dev _______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax


------------------------------------------------------------------------------
This SF.net email is sponsored by

Make an app they can't live without
Enter the BlackBerry Developer Challenge
http://p.sf.net/sfu/RIM-dev2dev 
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax