[Bioperl-l] seq features with locations on remote entries?

[Hilmar Lapp]

See Jason's email and FAQ 5.5

	http://www.bioperl.org/Core/Latest/FAQ.html#Q5.5

spliced_seq() goes and fetches the remote sequence if you pass it a 
RandomAccessI compliant object. perldoc Bio::SeqFeatureI and then 
search for spliced_seq.

	-hilmar

On Monday, July 7, 2003, at 07:59  AM, Matthew Betts wrote:

>
> Hi Hilmar,
>
> Thanks for that. I'm guessing that the best way to make sure that
> Bio::SeqFeature::Generic::seq gives back the whole of the sequence of a
> feature that has sub features with remote locations is to use
> Bio::Index to retrieve the remote sequence entries and then use
> Bio::SeqFeature::Generic::attach_seq?
>
> Thanks again,
>
> Matthew
>
> On Sat, 5 Jul 2003, Hilmar Lapp wrote:
>
>> All locations have a property $loc->is_remote(). The property
>> $loc->seq_id() gives what ultimately is supposed to serve as a URI or
>> LSID, but probably in most cases in just going to be the accession
>> number, possibly in accession.version notation.
>>
>> Quoted from the POD in Bio::LocationI:
>
> (snip)
>
> -- 
> Matthew Betts, mailto:matthew.betts at ii.uib.no
> Phone: (+47) 55 58 40 22
> Computational Biology Unit, BCCS,
> University of Bergen, N-5020 Bergen, Norway
>
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-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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