[Bioperl-l] Removing SeqFeatures

[Cook, Malcolm]

FWIW: In day's past I had the following exchange with
Ewan/Hilmar/Matthew on exactly this topic in which I proposed a patch to
Bio::Seq to define 'delete_SeqFeature' and was subsequenty converted
against the approach:

http://bioperl.org/pipermail/bioperl-l/2001-May/005624.html

Cheers,

malcolm


-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Marc Logghe
Sent: Thursday, June 02, 2005 8:24 AM
To: michael watson (IAH-C); Bioperl-l at portal.open-bio.org
Subject: RE: [Bioperl-l] Removing SeqFeatures


Hi Mick,
I think the only way is to run the remove_SeqFeatures() and catch the
removed features in an array.
Filter the array keeping the features you want to keep and add them to
your sequence object using 
add_SeqFeature(@features_to_keep)

HTH,
Marc

> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org 
> [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of 
> michael watson (IAH-C)
> Sent: Thursday, June 02, 2005 2:54 PM
> To: Bioperl-l at portal.open-bio.org
> Subject: [Bioperl-l] Removing SeqFeatures
> 
> Hi
> 
> I want to take an EMBL sequence and remove some of the 
> features, but keep all of the other information (accession, 
> id, sequence, comments etc).
> 
> So I have got some code which gives me the features that I 
> want and the ones I don't want, but I can't figure out how to 
> "remove" a feature.
> The only way I can think of doing this is to create a new 
> sequence and transfer the data across from the old sequence 
> bit by bit - surely there's a better way?
> 
> Many thanks
> 
> Mick
> 
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