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

Peng Yu pengyu.ut at gmail.com
Mon Jun 7 03:46:04 UTC 2010

On Sun, Jun 6, 2010 at 10:21 PM, Chris Fields <cjfields at illinois.edu> wrote:
> 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.

This explain sounds to abstract to me. Would you please give me some
examples on what it means?


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