Accessing Alias variable for links

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Accessing Alias variable for links

Scooter Willis-2
Accessing Alias variable for links
I would like to use the value of the Alias value in the gff3 track to build a custom external link. It does not appear that Alias is being exported. What gff3 attributes are being exported that I can use for building links to external servers? I am trying to associate a uniprot id with a predicted gene where I can’t use ID or Name because that has implied meaning. Alias seems like the proper use but does not appear to be working in gbrowse2. Happy to use a different variable name but can’t find any docs on what the options are.

Thanks

Scooter

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Re: Accessing Alias variable for links

Scott Cain
Hi Scooter,

You can use a perl callback to build the url, something like this:

link  = sub {
      my $f = shift;
      my ($alias) = $obj->get_tag_values('Alias') if $obj->has_tag('Alias');
      my $url = "http://google.com/?q=$alias";
      return $url;
  }

Scott


On Tue, Jun 15, 2010 at 10:37 AM, Scooter Willis <[hidden email]> wrote:

>
> I would like to use the value of the Alias value in the gff3 track to build
> a custom external link. It does not appear that Alias is being exported.
> What gff3 attributes are being exported that I can use for building links to
> external servers? I am trying to associate a uniprot id with a predicted
> gene where I can’t use ID or Name because that has implied meaning. Alias
> seems like the proper use but does not appear to be working in gbrowse2.
> Happy to use a different variable name but can’t find any docs on what the
> options are.
>
> Thanks
>
> Scooter
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> Gmod-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>
>



--
------------------------------------------------------------------------
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: Accessing Alias variable for links

Scooter Willis-2
Re: [GMOD-devel] Accessing Alias variable for links Thanks I will give it a try.


On 6/15/10 10:59 AM, "Scott Cain" <scott@...> wrote:

Hi Scooter,

You can use a perl callback to build the url, something like this:

link  = sub {
      my $f = shift;
      my ($alias) = $obj->get_tag_values('Alias') if $obj->has_tag('Alias');
      my $url = "http://google.com/?q=$alias";
      return $url;
  }

Scott


On Tue, Jun 15, 2010 at 10:37 AM, Scooter Willis <HWillis@...> wrote:
>
> I would like to use the value of the Alias value in the gff3 track to build
> a custom external link. It does not appear that Alias is being exported.
> What gff3 attributes are being exported that I can use for building links to
> external servers? I am trying to associate a uniprot id with a predicted
> gene where I can’t use ID or Name because that has implied meaning. Alias
> seems like the proper use but does not appear to be working in gbrowse2.
> Happy to use a different variable name but can’t find any docs on what the
> options are.
>
> Thanks
>
> Scooter
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> Gmod-devel mailing list
> Gmod-devel@...
> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>
>



--
------------------------------------------------------------------------
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: Accessing Alias variable for links

Scooter Willis-2
In reply to this post by Scott Cain
Re: [GMOD-devel] Accessing Alias variable for links Scott

If I have the following then I get the mouse pointer to change but it does not resolve the alias tag. If I replace with $name then it resolves to the name but it is not the name that uniprot understands.

link         = http://www.uniprot.org/uniprot/$alias

I tried the example below and results in no link being assigned to the glyph.

If I do this as an example then no link gets assigned. It appears the code is not being evaluated.

link         = sub {
        return 'http://www.uniprot.org';
        }

Any suggestions?

Thanks

Scooter


On 6/15/10 10:59 AM, "Scott Cain" <scott@...> wrote:

Hi Scooter,

You can use a perl callback to build the url, something like this:

link  = sub {
      my $f = shift;
      my ($alias) = $obj->get_tag_values('Alias') if $obj->has_tag('Alias');
      my $url = "http://google.com/?q=$alias";
      return $url;
  }

Scott


On Tue, Jun 15, 2010 at 10:37 AM, Scooter Willis <HWillis@...> wrote:
>
> I would like to use the value of the Alias value in the gff3 track to build
> a custom external link. It does not appear that Alias is being exported.
> What gff3 attributes are being exported that I can use for building links to
> external servers? I am trying to associate a uniprot id with a predicted
> gene where I can’t use ID or Name because that has implied meaning. Alias
> seems like the proper use but does not appear to be working in gbrowse2.
> Happy to use a different variable name but can’t find any docs on what the
> options are.
>
> Thanks
>
> Scooter
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> Gmod-devel mailing list
> Gmod-devel@...
> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>
>



--
------------------------------------------------------------------------
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: Accessing Alias variable for links

Scott Cain
Hi Scooter,

I'm ccing this to the GBrowse mailing list...

Certainly, the first thing you wrote won't work; there is no magic
$alias variable like the $name and $description variable for GBrowse
conf files.

The second thing should work though, unless this is in an uploaded GFF
file.  Does the apache error log give any indication that there is a
problem with processing that conf file?

Scott


On Wed, Jun 30, 2010 at 4:23 PM, Scooter Willis <[hidden email]> wrote:

> Scott
>
> If I have the following then I get the mouse pointer to change but it does
> not resolve the alias tag. If I replace with $name then it resolves to the
> name but it is not the name that uniprot understands.
>
> link         = http://www.uniprot.org/uniprot/$alias
>
> I tried the example below and results in no link being assigned to the
> glyph.
>
> If I do this as an example then no link gets assigned. It appears the code
> is not being evaluated.
>
> link         = sub {
>         return 'http://www.uniprot.org';
>         }
>
> Any suggestions?
>
> Thanks
>
> Scooter
>
>
> On 6/15/10 10:59 AM, "Scott Cain" <[hidden email]> wrote:
>
> Hi Scooter,
>
> You can use a perl callback to build the url, something like this:
>
> link  = sub {
>       my $f = shift;
>       my ($alias) = $obj->get_tag_values('Alias') if $obj->has_tag('Alias');
>       my $url = "http://google.com/?q=$alias";
>       return $url;
>   }
>
> Scott
>
>
> On Tue, Jun 15, 2010 at 10:37 AM, Scooter Willis <[hidden email]>
> wrote:
>>
>> I would like to use the value of the Alias value in the gff3 track to
>> build
>> a custom external link. It does not appear that Alias is being exported.
>> What gff3 attributes are being exported that I can use for building links
>> to
>> external servers? I am trying to associate a uniprot id with a predicted
>> gene where I can’t use ID or Name because that has implied meaning. Alias
>> seems like the proper use but does not appear to be working in gbrowse2.
>> Happy to use a different variable name but can’t find any docs on what the
>> options are.
>>
>> Thanks
>>
>> Scooter
>>
>> ------------------------------------------------------------------------------
>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> lucky parental unit.  See the prize list and enter to win:
>> http://p.sf.net/sfu/thinkgeek-promo
>> _______________________________________________
>> Gmod-devel mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
>



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