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

[Chris Fields]

On Jun 6, 2010, at 10:46 PM, Peng Yu wrote:

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

Like it says; the Location indicated may not be found in the current location or group of locations, but may be located remotely (in another sequence).  For instance:

http://www.ncbi.nlm.nih.gov/nuccore/13161546?report=genbank

BRCA2 has a split location, one located in this sequence record (AL137247), and one located remotely, in another sequence record (in AL445212.9):

join(AL445212.9:83662..166657,101..841)

In order to contain both of them together and have them splice correctly when needed, one must indicate that the sequence of interest for the location is not remote (is the current one) or is remote (and needs to be retrieved prior to additional work).

chris