[Bioperl-l] removing Seq features

hilmar.lapp@pharma.Novartis.com hilmar.lapp@pharma.Novartis.com
Wed, 18 Oct 2000 20:58:11 +0100

Interesting. For Generic features there is I think a flush_sub_SeqFeature()
or something similar, but it turns out to be absent from Seq. I guess this
has something to do with the supposed immutability of Seq objects, right
Ewan? Otherwise it's a bug.

We had a discussion some time ago about seq mutability. Given your context
of users dropping or adding features, you clearly need Seq objects as
mutable objects. I don't know how strongly Seq objects are supposed to be
immutable in BioPerl. Not least as you can change the sequence legally ...


Mark Wilkinson <mwilkinson@gene.pbi.nrc.ca>@bioperl.org on 18.10.2000

Sent by:  bioperl-l-admin@bioperl.org

To:   bioperl-l@bioperl.org
Subject:  [Bioperl-l] removing Seq features

hi group,

is there a 'formal' way to remove features from a Seq object?  I see
that there is an add_SeqFeature method for the Seq object, but there
appears to be no equlivalent remove_SeqFeature method.

If not, I presume it is sufficient just to delete this feature from the
hash 'by force'?  ...or?

Any advice appreciated!


Dr. Mark Wilkinson
Bioinformatics Group
National Research Council of Canada
Plant Biotechnology Institute
110 Gymnasium Place
Saskatoon, SK

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