search

dasmoth / dalliance

Interactive web-based genome browser.
http://www.biodalliance.org/
BSD 2-Clause "Simplified" License
227 stars 68 forks source link

Export features in region #20

Open greenexile4568 opened 13 years ago

greenexile4568 commented 13 years ago

Is there away or would it be possible to provide a mechanism whereby a user could highlight a range on the browser then export features found within that range on specific tracks ?

I have the browser embedded in our app and was hoping to be able to 'feed' any features of interest, identified during a user session back to the host application for further processing.

Thank you

dasmoth commented 13 years ago

This sounds like a generally useful feature. I guess there are two major parts:

   1) a region-selection mechanism (which we don't have yet, but probably should).

   2) a way to trigger the feature export/submit.

Do you have any particular feature table formats and/or target web services in mind? This could affect the implementation a bit. I believe Galaxy can receive "callbacks" from a browser, so might be worth looking at the protocols they use and asking if they can be adapted for your purposes.

greenexile4568 commented 13 years ago

For region selection I was thinking the user could click on the primary tram line, holding down the ctrl key to highlight a region. They could repeat this step multple times before clicking a new menu button 'Feature Set'

When this button is selected, a submenu would display a list of tracks (DAS & binary) from which to 'extract' features of interest. The features extracted would be stored in a simple object, leaving the transformation and transfer of this information to other webservices as an exercise for the programmer embedding the browser. While it might be possible to target a number of key services such as extending your current connectivity w/ UCSC browser, I think it would be expensive if you had to explictly build an interface to every possible system that might want callback info.

Looking for the simplest, non-invasive option ;) On 18 August 2011 04:06, dasmoth < reply@reply.github.com>wrote:

This sounds like a generally useful feature. I guess there are two major parts:

  1) a region-selection mechanism (which we don't have yet, but

probably should).

  2) a way to trigger the feature export/submit.

Do you have any particular feature table formats and/or target web services in mind? This could affect the implementation a bit. I believe Galaxy can receive "callbacks" from a browser, so might be worth looking at the protocols they use and asking if they can be adapted for your purposes.

Reply to this email directly or view it on GitHub: https://github.com/dasmoth/dalliance/issues/20#issuecomment-1837151

dasmoth commented 10 years ago

Renaming and bumping this because the export aspect of this is still unresolved, and would, I think, be a useful addition.

Some thought about what format(s) to support may be needed.

sinclaircooper commented 7 years ago

Has there been any progress been made on this issue? I would very much like to be able to extract features from a given selection. Extracting the features from the available tracks would be useful, failing that just being able to export the fasta sequence from an area of interest would also be very useful.