[Bioperl-l] Bio::SeqFeatureI spliced_seq

[Chris Fields]

There is a reported bug (Bug 2039) which I found an easy fix for; the issue
is that spliced_seq, as currently implemented, has two optional arguments:

my ($self, $db, $nosort) = @_;

$db is-a Bio::DB::RandomAccessI; $nosort is a flag so that locations aren't
sorted before splicing, which is crux of the bug.

So, to set $nosort you must also set $db to either undef or a
Bio::DB::RandomAccessI (a point not made in the docs and not immediately
clear to the user).  Would it make more sense to have something like this
(using $self->_rearrange to get the options)?

my $seq = $sf->spliced_seq(-nosort => 1);

my $seq = $sf->spliced_seq(-db => $db);

my $seq = $sf->spliced_seq(-nosort => 1
                           -db     => $db);

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign