[Bioperl-l] truncating a sequence and remapping annotations

[Chris Fields]

It's not implemented completely.  As Jason mentioned in the bug  
report, it was meant to be part of an overall system to truncate  
sequences with remapped features, but the implementation in place is  
substandard.  It's open for implementation if anyone wants to take it  
up.

I should point out, though, in my opinion Bio::DB::GFF/SeqFeature deal  
with this in a more elegant and lightweight way, and is probably the  
direction I would take.  YMMV.

chris

On Aug 27, 2009, at 12:40 PM, Robert Buels wrote:

> Looks like bug 1572 is related to this: http://bugzilla.open-bio.org/show_bug.cgi?id=1572
>
> Rob
>
> Robert Buels wrote:
>> Hi all,
>> Recently a user came into #bioperl looking to truncate an annotated  
>> sequence (leaving the region between e.g. 150 to 250 nt), and have  
>> the annotations from the original sequence be remapped onto the new  
>> truncated sequence.
>> Poking through code, I came across an undocumented function trunc()  
>> that from the comments looks like it was written by Jason as part  
>> of a master plan to implement this very functionality.
>> Just wondering, what's the status of that?
>> Rob
>
>
> -- 
> Robert Buels
> Bioinformatics Analyst, Sol Genomics Network
> Boyce Thompson Institute for Plant Research
> Tower Rd
> Ithaca, NY  14853
> Tel: 503-889-8539
> rmb32 at cornell.edu
> http://www.sgn.cornell.edu
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