[Gmod-ajax] Jump to next feature?

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

[Gmod-ajax] Jump to next feature?

Ben Bimber
Hello,

I have a bed file with relatively sparse features, spread over the genome.  I added this as a track in JBrowse.  I'd like to let the user iterate these features, viewing one, and then quickly jumping to the next (which might be far away).  Is there a good way for a user to do this in JBrowse?

Thanks,
Ben

------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://makebettercode.com/inteldaal-eval
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
Reply | Threaded
Open this post in threaded view
|

Re: Jump to next feature?

Colin
Hi Ben,

We actually have this feature in Apollo for the annotation track, which uses a keyboard shortcut { and } to scroll to the prev/next annotation feature. It is specific to the features on the annotation track, and it is possible because all annotation data is loaded at once. In general though, for jbrowse tracks, the data is loaded on demand, so that data isn't available.

Conceivably, you could
(a) use Apollo for this somehow, for example by loading your BED features onto the annotation track or something similar, to take advantage of Apollo's existing functionality.
(b) make a custom store class that downloads the data for the whole chromosome at a time, and do something similar to Apollo!


Let me know if that helps


(sorry for duplicate message, posted without including list)


-Colin

On Mon, Mar 7, 2016 at 12:30 PM, Ben Bimber <[hidden email]> wrote:
Hello,

I have a bed file with relatively sparse features, spread over the genome.  I added this as a track in JBrowse.  I'd like to let the user iterate these features, viewing one, and then quickly jumping to the next (which might be far away).  Is there a good way for a user to do this in JBrowse?

Thanks,
Ben

------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://makebettercode.com/inteldaal-eval
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://makebettercode.com/inteldaal-eval
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
Reply | Threaded
Open this post in threaded view
|

Re: Jump to next feature?

Keiran Raine
Hi,

IMO the ability to load a BED file of ROI (to use IGV terminology) and step through is something that should be in the base JBrowse install.  It’s something that is available in IGV and often queried by our users.

Yes we know it can be done by wrapping JBrowse, we’ve done it previously (and submitted patches related to it).

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 8 Mar 2016, at 18:35, Colin <[hidden email]> wrote:

Hi Ben,

We actually have this feature in Apollo for the annotation track, which uses a keyboard shortcut { and } to scroll to the prev/next annotation feature. It is specific to the features on the annotation track, and it is possible because all annotation data is loaded at once. In general though, for jbrowse tracks, the data is loaded on demand, so that data isn't available.

Conceivably, you could
(a) use Apollo for this somehow, for example by loading your BED features onto the annotation track or something similar, to take advantage of Apollo's existing functionality.
(b) make a custom store class that downloads the data for the whole chromosome at a time, and do something similar to Apollo!


Let me know if that helps


(sorry for duplicate message, posted without including list)


-Colin

On Mon, Mar 7, 2016 at 12:30 PM, Ben Bimber <[hidden email]> wrote:
Hello,

I have a bed file with relatively sparse features, spread over the genome.  I added this as a track in JBrowse.  I'd like to let the user iterate these features, viewing one, and then quickly jumping to the next (which might be far away).  Is there a good way for a user to do this in JBrowse?

Thanks,
Ben

------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://makebettercode.com/inteldaal-eval
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax


------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://makebettercode.com/inteldaal-eval
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax


------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://makebettercode.com/inteldaal-eval
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

smime.p7s (2K) Download Attachment
Reply | Threaded
Open this post in threaded view
|

Re: Jump to next feature?

Colin
Hi Keiran

Maybe this github thread might be related! https://github.com/GMOD/jbrowse/issues/194

Then maybe if the data that Ben mentioned was being used, it could be loaded into such a tool (i.e. the import from text file note on the github thread)

-Colin

On Tue, Mar 8, 2016 at 12:50 PM, Keiran Raine <[hidden email]> wrote:
Hi,

IMO the ability to load a BED file of ROI (to use IGV terminology) and step through is something that should be in the base JBrowse install.  It’s something that is available in IGV and often queried by our users.

Yes we know it can be done by wrapping JBrowse, we’ve done it previously (and submitted patches related to it).

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:<a href="tel:%2B44%20%280%291223%20834244%20Ext%3A%207703" value="+441223834244" target="_blank">+44 (0)1223 834244 Ext: 7703
Office: H104

On 8 Mar 2016, at 18:35, Colin <[hidden email]> wrote:

Hi Ben,

We actually have this feature in Apollo for the annotation track, which uses a keyboard shortcut { and } to scroll to the prev/next annotation feature. It is specific to the features on the annotation track, and it is possible because all annotation data is loaded at once. In general though, for jbrowse tracks, the data is loaded on demand, so that data isn't available.

Conceivably, you could
(a) use Apollo for this somehow, for example by loading your BED features onto the annotation track or something similar, to take advantage of Apollo's existing functionality.
(b) make a custom store class that downloads the data for the whole chromosome at a time, and do something similar to Apollo!


Let me know if that helps


(sorry for duplicate message, posted without including list)


-Colin

On Mon, Mar 7, 2016 at 12:30 PM, Ben Bimber <[hidden email]> wrote:
Hello,

I have a bed file with relatively sparse features, spread over the genome.  I added this as a track in JBrowse.  I'd like to let the user iterate these features, viewing one, and then quickly jumping to the next (which might be far away).  Is there a good way for a user to do this in JBrowse?

Thanks,
Ben

------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://makebettercode.com/inteldaal-eval
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax


------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://makebettercode.com/inteldaal-eval
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://makebettercode.com/inteldaal-eval
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
Reply | Threaded
Open this post in threaded view
|

Re: Jump to next feature?

Keiran Raine
Hi Colin,

Looks like one of the other features promised in the GMOD 2014 meeting for 2.0 (I know Robert left quite soon after though).

Cheers,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 8 Mar 2016, at 20:21, Colin <[hidden email]> wrote:

Hi Keiran

Maybe this github thread might be related! https://github.com/GMOD/jbrowse/issues/194

Then maybe if the data that Ben mentioned was being used, it could be loaded into such a tool (i.e. the import from text file note on the github thread)

-Colin

On Tue, Mar 8, 2016 at 12:50 PM, Keiran Raine <[hidden email]> wrote:
Hi,

IMO the ability to load a BED file of ROI (to use IGV terminology) and step through is something that should be in the base JBrowse install.  It’s something that is available in IGV and often queried by our users.

Yes we know it can be done by wrapping JBrowse, we’ve done it previously (and submitted patches related to it).

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:<a href="tel:%2B44%20%280%291223%20834244%20Ext%3A%207703" value="+441223834244" target="_blank" class="">+44 (0)1223 834244 Ext: 7703
Office: H104

On 8 Mar 2016, at 18:35, Colin <[hidden email]> wrote:

Hi Ben,

We actually have this feature in Apollo for the annotation track, which uses a keyboard shortcut { and } to scroll to the prev/next annotation feature. It is specific to the features on the annotation track, and it is possible because all annotation data is loaded at once. In general though, for jbrowse tracks, the data is loaded on demand, so that data isn't available.

Conceivably, you could
(a) use Apollo for this somehow, for example by loading your BED features onto the annotation track or something similar, to take advantage of Apollo's existing functionality.
(b) make a custom store class that downloads the data for the whole chromosome at a time, and do something similar to Apollo!


Let me know if that helps


(sorry for duplicate message, posted without including list)


-Colin

On Mon, Mar 7, 2016 at 12:30 PM, Ben Bimber <[hidden email]> wrote:
Hello,

I have a bed file with relatively sparse features, spread over the genome.  I added this as a track in JBrowse.  I'd like to let the user iterate these features, viewing one, and then quickly jumping to the next (which might be far away).  Is there a good way for a user to do this in JBrowse?

Thanks,
Ben

------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://makebettercode.com/inteldaal-eval
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax


------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://makebettercode.com/inteldaal-eval
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
Reply | Threaded
Open this post in threaded view
|

Re: Jump to next feature?

Ben Bimber
Hi guys,

To recap what Keiran wrote: "IMO the ability to load a BED file of ROI (to use IGV terminology) and step through is something that should be in the base JBrowse install."

I think there's 2 features there:

1) load a BED
2) step through a track feature-by-feature once loaded.

At least for us, #2 is really what we're after, and I'd also argue this is a pretty general purpose feature that really ought to be available to any jbrowse track.  The reason we have users bringing this up is that when you have a sparse track with distant features, simply scanning downstream isnt very appealing.  

I might explore what could be done w/ plugins.  Keiran, if you think you have existing code or pull requests that touch on this, I'd appreciate any pointers.  

I understand the full track data isnt loaded client-side on jbrowse; however, are there any APIs to query tracks besides position?  In theory one could iterate down the genome until we find a feature and then re-center on that coordinate, but that's ugly.

-Ben

On Wed, Mar 9, 2016 at 1:01 AM, Keiran Raine <[hidden email]> wrote:
Hi Colin,

Looks like one of the other features promised in the GMOD 2014 meeting for 2.0 (I know Robert left quite soon after though).

Cheers,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:<a href="tel:%2B44%20%280%291223%20834244%20Ext%3A%207703" value="+441223834244" target="_blank">+44 (0)1223 834244 Ext: 7703
Office: H104

On 8 Mar 2016, at 20:21, Colin <[hidden email]> wrote:

Hi Keiran

Maybe this github thread might be related! https://github.com/GMOD/jbrowse/issues/194

Then maybe if the data that Ben mentioned was being used, it could be loaded into such a tool (i.e. the import from text file note on the github thread)

-Colin

On Tue, Mar 8, 2016 at 12:50 PM, Keiran Raine <[hidden email]> wrote:
Hi,

IMO the ability to load a BED file of ROI (to use IGV terminology) and step through is something that should be in the base JBrowse install.  It’s something that is available in IGV and often queried by our users.

Yes we know it can be done by wrapping JBrowse, we’ve done it previously (and submitted patches related to it).

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:<a href="tel:%2B44%20%280%291223%20834244%20Ext%3A%207703" value="+441223834244" target="_blank">+44 (0)1223 834244 Ext: 7703
Office: H104

On 8 Mar 2016, at 18:35, Colin <[hidden email]> wrote:

Hi Ben,

We actually have this feature in Apollo for the annotation track, which uses a keyboard shortcut { and } to scroll to the prev/next annotation feature. It is specific to the features on the annotation track, and it is possible because all annotation data is loaded at once. In general though, for jbrowse tracks, the data is loaded on demand, so that data isn't available.

Conceivably, you could
(a) use Apollo for this somehow, for example by loading your BED features onto the annotation track or something similar, to take advantage of Apollo's existing functionality.
(b) make a custom store class that downloads the data for the whole chromosome at a time, and do something similar to Apollo!


Let me know if that helps


(sorry for duplicate message, posted without including list)


-Colin

On Mon, Mar 7, 2016 at 12:30 PM, Ben Bimber <[hidden email]> wrote:
Hello,

I have a bed file with relatively sparse features, spread over the genome.  I added this as a track in JBrowse.  I'd like to let the user iterate these features, viewing one, and then quickly jumping to the next (which might be far away).  Is there a good way for a user to do this in JBrowse?

Thanks,
Ben

------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://makebettercode.com/inteldaal-eval
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax


------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://makebettercode.com/inteldaal-eval
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.


------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
Reply | Threaded
Open this post in threaded view
|

Re: Jump to next feature?

Keiran Raine
Hi Ben,

What we (as a group) implemented was control of an embedded JBrowse, it’s clunky and awful for small screens.  I thought one of our devs implemented it, but it looks like the final implementation was actually done by Colin in the end:




Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 9 Mar 2016, at 14:31, Ben Bimber <[hidden email]> wrote:

Hi guys,

To recap what Keiran wrote: "IMO the ability to load a BED file of ROI (to use IGV terminology) and step through is something that should be in the base JBrowse install."

I think there's 2 features there:

1) load a BED
2) step through a track feature-by-feature once loaded.

At least for us, #2 is really what we're after, and I'd also argue this is a pretty general purpose feature that really ought to be available to any jbrowse track.  The reason we have users bringing this up is that when you have a sparse track with distant features, simply scanning downstream isnt very appealing.  

I might explore what could be done w/ plugins.  Keiran, if you think you have existing code or pull requests that touch on this, I'd appreciate any pointers.  

I understand the full track data isnt loaded client-side on jbrowse; however, are there any APIs to query tracks besides position?  In theory one could iterate down the genome until we find a feature and then re-center on that coordinate, but that's ugly.

-Ben

On Wed, Mar 9, 2016 at 1:01 AM, Keiran Raine <[hidden email]> wrote:
Hi Colin,

Looks like one of the other features promised in the GMOD 2014 meeting for 2.0 (I know Robert left quite soon after though).

Cheers,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:<a href="tel:%2B44%20%280%291223%20834244%20Ext%3A%207703" value="+441223834244" target="_blank" class="">+44 (0)1223 834244 Ext: 7703
Office: H104

On 8 Mar 2016, at 20:21, Colin <[hidden email]> wrote:

Hi Keiran

Maybe this github thread might be related! https://github.com/GMOD/jbrowse/issues/194

Then maybe if the data that Ben mentioned was being used, it could be loaded into such a tool (i.e. the import from text file note on the github thread)

-Colin

On Tue, Mar 8, 2016 at 12:50 PM, Keiran Raine <[hidden email]> wrote:
Hi,

IMO the ability to load a BED file of ROI (to use IGV terminology) and step through is something that should be in the base JBrowse install.  It’s something that is available in IGV and often queried by our users.

Yes we know it can be done by wrapping JBrowse, we’ve done it previously (and submitted patches related to it).

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:<a href="tel:%2B44%20%280%291223%20834244%20Ext%3A%207703" value="+441223834244" target="_blank" class="">+44 (0)1223 834244 Ext: 7703
Office: H104

On 8 Mar 2016, at 18:35, Colin <[hidden email]> wrote:

Hi Ben,

We actually have this feature in Apollo for the annotation track, which uses a keyboard shortcut { and } to scroll to the prev/next annotation feature. It is specific to the features on the annotation track, and it is possible because all annotation data is loaded at once. In general though, for jbrowse tracks, the data is loaded on demand, so that data isn't available.

Conceivably, you could
(a) use Apollo for this somehow, for example by loading your BED features onto the annotation track or something similar, to take advantage of Apollo's existing functionality.
(b) make a custom store class that downloads the data for the whole chromosome at a time, and do something similar to Apollo!


Let me know if that helps


(sorry for duplicate message, posted without including list)


-Colin

On Mon, Mar 7, 2016 at 12:30 PM, Ben Bimber <[hidden email]> wrote:
Hello,

I have a bed file with relatively sparse features, spread over the genome.  I added this as a track in JBrowse.  I'd like to let the user iterate these features, viewing one, and then quickly jumping to the next (which might be far away).  Is there a good way for a user to do this in JBrowse?

Thanks,
Ben

------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://makebettercode.com/inteldaal-eval
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax


------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://makebettercode.com/inteldaal-eval
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.



-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax