[Bioperl-l] Bio::Location::Simple's is_remote() missing?

[Chris Fields]

On Jun 6, 2010, at 8:25 PM, Peng Yu wrote:

> It is not clear to me what is_remote is for in Bio::Location::Simple.
> Neither the perldoc or the following webpage discuss what it means.
> 
> http://www.bioperl.org/wiki/BioPerl_Locations

As explained at the top of that page, it is a spec page that explains some things about locations, but is nowhere near complete. In fact, I almost forgot I wrote that up years ago.  Huh.

is_remote() is just a boolean indicating the location is_remote (is located on a remote sequence).  That is one thing that needs additional documentation (see below).

> $ is_remote/main.pl
> Use of uninitialized value in print at is_remote/main.pl line 11.
> $ cat is_remote/main.pl
> #!/usr/bin/env perl
> 
> use strict;
> use warnings;
> 
> use Bio::Location::Simple;
> 
> my $location = Bio::Location::Simple->new(-start => 1, -end => 100,
>  -strand => 1 );
> 
> print $location->is_remote(), "\n";
> 
> ########
> I looked at the source code Simple.pm. I don't see is_remote() is
> defined in it. Is it deprecate? Should the document for it be removed?
> 
> -- 
> Regards,
> Peng


No, it isn't deprecated, but is defined in the base class Bio::Location::Atomic.  

Here is the relevant documentation in Bio::LocationI, has just been updated in the implementations on github:

 Title   : is_remote
 Usage   : $is_remote_loc = $loc->is_remote()
 Function: Whether or not a location is a remote location.

           A location is said to be remote if it is on a different
           'object' than the object which 'has' this
           location. Typically, features on a sequence will sometimes
           have a remote location, which means that the location of
           the feature is on a different sequence than the one that is
           attached to the feature. In such a case, $loc->seq_id will
           be different from $feat->seq_id (usually they will be the
           same).

           While this may sound weird, it reflects the location of the
           kind of AB18375:450-900 which can be found in GenBank/EMBL
           feature tables.

 Example : 
 Returns : TRUE if the location is a remote location, and FALSE otherwise
 Args    : Value to set to

chris