[Bioperl-l] Bio::Location::Simple's is_remote() missing?
cjfields at illinois.edu
Sun Jun 6 23:21:56 EDT 2010
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.
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?
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
While this may sound weird, it reflects the location of the
kind of AB18375:450-900 which can be found in GenBank/EMBL
Returns : TRUE if the location is a remote location, and FALSE otherwise
Args : Value to set to
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