Mapping "chr2" -> "2" (etc) for uploaded wig/bigwig files

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

Mapping "chr2" -> "2" (etc) for uploaded wig/bigwig files

Kevin Schaper-2
I'm working on upgrading ZFIN's GBrowse to 2.x, primarily so that we'll have support for wiggle tracks.   We're mainly interested in allowing users to upload tracks.   The published wiggle tracks we've looked at have all used the UCSC chromosome naming convention with the chr prefix, but that's not what we use - is there a way to strip the chr from chromosome names at upload time?

thanks,
Kevin




------------------------------------------------------------------------------
DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps
OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access
Free app hosting. Or install the open source package on any LAMP server.
Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native!
http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: Mapping "chr2" -> "2" (etc) for uploaded wig/bigwig files

Timothy Parnell
Hi Kevin,

GBrowse, it appears, is smart enough to automatically prepend "chr" when I enter a coordinate query without one. This is using a SeqFeature::Store database that contains "chr" chromosomes and bigwig files with the same. I have not tried the converse (database without "chr"), but I suspect it can handle it.

With regards to uploads, there is an option you can put in the data source conf general section that does this: seqid_prefix. There is more info on the GMOD wiki GBrowse how to, but if you set this to "chr", then it should automatically adjust the prefix uploaded text files (bed, gff, text wig files). Binary files, on the other hand, will not be affected by this parameter. It would be too expensive to modify binary files directly upon upload. But hopefully coordinate queries by GBrowse can handle it appropriately.

Tim

On Nov 15, 2013, at 3:21 PM, Kevin Schaper <[hidden email]> wrote:

> I'm working on upgrading ZFIN's GBrowse to 2.x, primarily so that we'll have support for wiggle tracks.   We're mainly interested in allowing users to upload tracks.   The published wiggle tracks we've looked at have all used the UCSC chromosome naming convention with the chr prefix, but that's not what we use - is there a way to strip the chr from chromosome names at upload time?
>
> thanks,
> Kevin
>
>
>
> ------------------------------------------------------------------------------
> DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps
> OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access
> Free app hosting. Or install the open source package on any LAMP server.
> Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native!
> http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk_______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps
OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access
Free app hosting. Or install the open source package on any LAMP server.
Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native!
http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: Mapping "chr2" -> "2" (etc) for uploaded wig/bigwig files

Timothy Parnell
In reply to this post by Kevin Schaper-2
Hi Kevin,

GBrowse, it appears, is smart enough to automatically prepend "chr" when I enter a coordinate query without one. This is using a SeqFeature::Store database that contains "chr" chromosomes and bigwig files with the same. I have not tried the converse (database without "chr"), but I suspect it can handle it.

With regards to uploads, there is an option you can put in the data source conf general section that does this: seqid_prefix. There is more info on the GMOD wiki GBrowse how to, but if you set this to "chr", then it should automatically adjust the prefix uploaded text files (bed, gff, text wig files). Binary files, on the other hand, will not be affected by this parameter. It would be too expensive to modify binary files directly upon upload. But hopefully coordinate queries by GBrowse can handle it appropriately.

Tim

On Nov 15, 2013, at 3:21 PM, Kevin Schaper <[hidden email]> wrote:

> I'm working on upgrading ZFIN's GBrowse to 2.x, primarily so that we'll have support for wiggle tracks.   We're mainly interested in allowing users to upload tracks.   The published wiggle tracks we've looked at have all used the UCSC chromosome naming convention with the chr prefix, but that's not what we use - is there a way to strip the chr from chromosome names at upload time?
>
> thanks,
> Kevin
>
>
>
> ------------------------------------------------------------------------------
> DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps
> OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access
> Free app hosting. Or install the open source package on any LAMP server.
> Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native!
> http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk_______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps
OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access
Free app hosting. Or install the open source package on any LAMP server.
Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native!
http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: Mapping "chr2" -> "2" (etc) for uploaded wig/bigwig files

Kevin Schaper-3
In reply to this post by Timothy Parnell
Yup 

seqid_prefix=chr   

Strips them on the way into my "chr"less database.  

Thanks Tim!






On Mon, Nov 18, 2013 at 8:20 AM, Timothy Parnell <[hidden email]> wrote:
Hi Kevin,

GBrowse, it appears, is smart enough to automatically prepend "chr" when I enter a coordinate query without one. This is using a SeqFeature::Store database that contains "chr" chromosomes and bigwig files with the same. I have not tried the converse (database without "chr"), but I suspect it can handle it.

With regards to uploads, there is an option you can put in the data source conf general section that does this: seqid_prefix. There is more info on the GMOD wiki GBrowse how to, but if you set this to "chr", then it should automatically adjust the prefix uploaded text files (bed, gff, text wig files). Binary files, on the other hand, will not be affected by this parameter. It would be too expensive to modify binary files directly upon upload. But hopefully coordinate queries by GBrowse can handle it appropriately.

Tim

On Nov 15, 2013, at 3:21 PM, Kevin Schaper <[hidden email]> wrote:

> I'm working on upgrading ZFIN's GBrowse to 2.x, primarily so that we'll have support for wiggle tracks.   We're mainly interested in allowing users to upload tracks.   The published wiggle tracks we've looked at have all used the UCSC chromosome naming convention with the chr prefix, but that's not what we use - is there a way to strip the chr from chromosome names at upload time?
>
> thanks,
> Kevin
>
>
>
> ------------------------------------------------------------------------------
> DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps
> OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access
> Free app hosting. Or install the open source package on any LAMP server.
> Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native!
> http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk_______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




------------------------------------------------------------------------------
Shape the Mobile Experience: Free Subscription
Software experts and developers: Be at the forefront of tech innovation.
Intel(R) Software Adrenaline delivers strategic insight and game-changing
conversations that shape the rapidly evolving mobile landscape. Sign up now.
http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse