[Bioperl-l] [Gmod-gbrowse] Bio::DB::GFF and feature order

Lincoln Stein lincoln.stein at gmail.com
Thu Nov 2 15:41:06 EST 2006


How do you want them sorted? To sort them by their start positions:

  my @CDS = sort {$a->start<=>$b->start} $segment->features('CDS');

Other people may want to sort features by end position, length, name, or who
knows what.

Lincoln

On 11/2/06, Andrew Stewart <stewarta at nmrc.navy.mil> wrote:
>
> In attempting to determine some statistics on the distances between CDS
> features in my Bio::DB::GFF database, I ran a query on all CDS features as
> follows...
> my @CDS = $segment->features('CDS');
>
> ...only to find that the features returned are not in order.  Is there a
> way of returning the features in order or sorting them through some internal
> Bio::DB::GFF related method, aside from the more obvious  path of sorting
> through the array itself (somehow)?
>
>
> -A
>
> --
> Andrew Stewart
> Research Assistant, Genomics Team
> Navy Medical Research Center (NMRC)
> Biological Defense Research Directorate (BDRD)
> BDRD Annex
> 12300 Washington Avenue, 2nd Floor
> Rockville, MD 20852
>
> email: stewarta at nmrc.navy.mil
> phone: 301-231-6700 Ext 270
>
>
>
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job
> easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>


-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
FOR URGENT MESSAGES & SCHEDULING,
PLEASE CONTACT MY ASSISTANT,
SANDRA MICHELSEN, AT michelse at cshl.edu


More information about the Bioperl-l mailing list