[Gmod-ajax] Indexing of transcript names in genes

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[Gmod-ajax] Indexing of transcript names in genes

Mikael Brandström Durling
Hi,

is it possible to make generate names index transcript names in a gene? Currently I only get autocompletion of gene names in the search box, while in many cases I would like to be able to search for specific transcripts of gene models with different isoforms predicted.

Thanks for a very nice browser!

Mikael


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Re: Indexing of transcript names in genes

Robert Buels-2
Name indexing only operates on top-level features right now.  The
easiest thing to do would probably be to add the transcript names as
Alias attributes to the top-level gene features.

Or, if you have some Perl programming skills, I'd be happy to see a pull
request on GitHub that added a --subfeatureNames option to
flatfile-to-json.pl that output name-indexing records for subfeatures.
That would more directly address this.


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 02/21/2014 08:30 AM, Mikael Brandström Durling wrote:

> Hi,
>
> is it possible to make generate names index transcript names in a gene? Currently I only get autocompletion of gene names in the search box, while in many cases I would like to be able to search for specific transcripts of gene models with different isoforms predicted.
>
> Thanks for a very nice browser!
>
> Mikael
>
>
> ------------------------------------------------------------------------------
> Managing the Performance of Cloud-Based Applications
> Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
> Read the Whitepaper.
> http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk
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>

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Re: Indexing of transcript names in genes

Mikael Brandström Durling

21 feb 2014 kl. 14:39 skrev Robert Buels <[hidden email]>:

> Name indexing only operates on top-level features right now.  The easiest thing to do would probably be to add the transcript names as Alias attributes to the top-level gene features.

Ok. Might be as hard to implement as your second alternative, while the alternative below would be much more general.

>
> Or, if you have some Perl programming skills, I'd be happy to see a pull request on GitHub that added a --subfeatureNames option to flatfile-to-json.pl that output name-indexing records for subfeatures. That would more directly address this.
>

I might give this one a shot. Just had a brief look into the source trying to figure where the name string was generated. I suppose it is flatten_to_names in Bio::JBrowse::FeatureStream that needs to be extend to look into sub features in this case?

Cheers,
Mikael



>
> Robert Buels
> Lead Developer
> JBrowse - http://jbrowse.org
>
> On 02/21/2014 08:30 AM, Mikael Brandström Durling wrote:
>> Hi,
>>
>> is it possible to make generate names index transcript names in a gene? Currently I only get autocompletion of gene names in the search box, while in many cases I would like to be able to search for specific transcripts of gene models with different isoforms predicted.
>>
>> Thanks for a very nice browser!
>>
>> Mikael
>>
>>
>> ------------------------------------------------------------------------------
>> Managing the Performance of Cloud-Based Applications
>> Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
>> Read the Whitepaper.
>> http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk
>> _______________________________________________
>> Gmod-ajax mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>


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Re: Indexing of transcript names in genes

Robert Buels-2
On 02/21/2014 09:26 AM, Mikael Brandström Durling wrote:
> I might give this one a shot. Just had a brief look into the source trying to figure where the name string was generated. I suppose it is flatten_to_names in Bio::JBrowse::FeatureStream that needs to be extend to look into sub features in this case?

Yes, that's probably it!  Thanks for your help!



Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

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