[Bioperl-l] Sub Seq Feature help

Brian Osborne brian_osborne at cognia.com
Fri Feb 6 07:38:01 EST 2004


There may be useful example code for you in the Feature-Annotation HOWTO
(http://bioperl.org/HOWTOs/html/Feature-Annotation.html) or in the FAQ

Brian O.

-----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
Sent: Friday, February 06, 2004 5:32 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] Sub Seq Feature help


I want to manipulate the start and end position of a CDS feature that looks
like this:

FT      CDS     join(2307..3221,1..1623)

I have tried:

my @features = $seq->get_all_SeqFeatures;
foreach $f (@features) {
        my @subs = $f->sub_SeqFeature;
        foreach $s (@subs) {
                print $s->start, "-", $s->end, "\n";

However, I get nothing out.  The code doesn't descend into the sub seq
features as $f->sub_SeqFeature doesn't return anything.  Nor does

Clearly I am doing something wrong, but what?  I am using Bioperl-1.2.3

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