[Bioperl-l] BioPerl newbie question about exporting sub_SeqFeatures

[gert thijs]

Concerning this bug, I can refer to bugreport 930 that I submitted a few weeks
ago and also to an email I posted on this list:
Subject: [Bioperl-l] Re: [Bioperl-guts-l] Notification: incoming/930 (fwd)
Date: Wed, 28 Mar 2001 18:02:59 +0200

This is a short description of the problem:
I have a script to downloaded a sequence from GenBank, store it in a Bio::Seq
and finally write it to a file. Later I would like to reread this sequence
form the file. But there is a problem in writing the correct location, when
the original location looks like 'complement(join(1..100,200..300,400..500))', 
the printed location would look like:
'complement(join(complement(1..100),200..300,400..500))'

Gert Thijs


Ewan Birney wrote:
> 
> Guys -
> 
> the "real" bug here in some sense is that Mark is not using
> SplitLocations, and, in addition, that what "sub_SeqFeatures" mean
> relative to a Split Location is really ill defined, and/or that the whole
> mapping of "complex object" to EMBL/GenBank is a ... semantic mire.
> 
> Mark - what do you actually want to do? It may wellbe that you want to be
> introduced to the wonders of the to_FTHelper function which will give you
> full control of the way your features is dumped in EMBL and GenBank
> format.
> 
> e.
> 
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>.
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-- 
+ Gert Thijs              
+ 
+ email: gert.thijs@esat.kuleuven.ac.be 
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