[Gmod-ajax] Filter track on the fly

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[Gmod-ajax] Filter track on the fly

FredBGA

Hello

 

I would like to be able to filter a track on the fly (on gff3 based tracks).

 

The use case would be : for a gene model track, with an attribute Confidence (high, low, medium) I would like to filter this track based on this attribute

I’m a user of the “former” GBrowse, and its subtrack option : http://gmod.org/wiki/GBrowse_2.0_HOWTO#Subtrack_Creation_Options. And it was great to be able to add three subtracks in this example.

 

I saw that JBrowse 1.10.4 has added a way to filter a VCF based track :

Added checkboxes to HTMLVariants and CanvasVariants track menus that allow filtering displayed features based on the FILTER attribute in a VCF file (https://jbrowse.org/jbrowse-1-10-4/)

 

Do you think it could be possible to do something like that ?

The user can enter an attribute name, a value and choose an operator (equals, greater than, contains etc.).

 

Thank you for your help and your ideas.

 

---

Fred

 


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Re: Filter track on the fly

Colin
The link that you mention about filtering for VCF tracks is pretty good point of reference. There is sort of a generic filtering "API" that was probably added with that release.

Just as a demo, I made something to demo the filtering "API" as a plugin, and added some instructions on github https://github.com/cmdcolin/filterplugin/

 It would actually be cool if the feature filters could be defined in a config file, but that isn't there yet. Maybe this plugin could be extended to allow you to define those, but you can use the code as a reference by itself too.

-Colin 

On Fri, Nov 25, 2016 at 9:58 AM, SAPET, Frederic <[hidden email]> wrote:

Hello

 

I would like to be able to filter a track on the fly (on gff3 based tracks).

 

The use case would be : for a gene model track, with an attribute Confidence (high, low, medium) I would like to filter this track based on this attribute

I’m a user of the “former” GBrowse, and its subtrack option : http://gmod.org/wiki/GBrowse_2.0_HOWTO#Subtrack_Creation_Options. And it was great to be able to add three subtracks in this example.

 

I saw that JBrowse 1.10.4 has added a way to filter a VCF based track :

Added checkboxes to HTMLVariants and CanvasVariants track menus that allow filtering displayed features based on the FILTER attribute in a VCF file (https://jbrowse.org/jbrowse-1-10-4/)

 

Do you think it could be possible to do something like that ?

The user can enter an attribute name, a value and choose an operator (equals, greater than, contains etc.).

 

Thank you for your help and your ideas.

 

---

Fred

 


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Re: Filter track on the fly

FredBGA

Hello Colin,

 

Thank you for your answer.

I will take a look to your link.

 

Fred

 

De : Colin [mailto:[hidden email]]
Envoyé : vendredi 25 novembre 2016 21:22
À : SAPET, Frederic <[hidden email]>
Cc : [hidden email]
Objet : Re: [Gmod-ajax] Filter track on the fly

 

The link that you mention about filtering for VCF tracks is pretty good point of reference. There is sort of a generic filtering "API" that was probably added with that release.

 

Just as a demo, I made something to demo the filtering "API" as a plugin, and added some instructions on github https://github.com/cmdcolin/filterplugin/

 

 It would actually be cool if the feature filters could be defined in a config file, but that isn't there yet. Maybe this plugin could be extended to allow you to define those, but you can use the code as a reference by itself too.

 

-Colin 

 

On Fri, Nov 25, 2016 at 9:58 AM, SAPET, Frederic <[hidden email]> wrote:

Hello

 

I would like to be able to filter a track on the fly (on gff3 based tracks).

 

The use case would be : for a gene model track, with an attribute Confidence (high, low, medium) I would like to filter this track based on this attribute

I’m a user of the “former” GBrowse, and its subtrack option : http://gmod.org/wiki/GBrowse_2.0_HOWTO#Subtrack_Creation_Options. And it was great to be able to add three subtracks in this example.

 

I saw that JBrowse 1.10.4 has added a way to filter a VCF based track :

Added checkboxes to HTMLVariants and CanvasVariants track menus that allow filtering displayed features based on the FILTER attribute in a VCF file (https://jbrowse.org/jbrowse-1-10-4/)

 

Do you think it could be possible to do something like that ?

The user can enter an attribute name, a value and choose an operator (equals, greater than, contains etc.).

 

Thank you for your help and your ideas.

 

---

Fred

 


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