[Bioperl-l] Bio::Tools::Glimmer and genes wrapping around the origin

[Francisco J. Ossandón]

Long ago, Bio::SeqIO had an issue with genes that were split at the origin.
This was because Bioperl, when reading a Genbank file, automatically sorted
the segments coordinates of the genes that was reading (not considering the
possibility in a circular genome, where the sequence could go from the 1st
nucleotide directly to the last one), so an extra "-nosort" argument was
necessary every time to avoid Bioperl giving the wrong sequence:

my $ nt_seq_obj = $feat->spliced_seq(-nosort => 1);

This is the same bug. In that case the code was changed so the "-nosort"
were applied based on the status of "is_circular" of the genome, see here:
https://redmine.open-bio.org/issues/2579

Since your code don't have the "is_circular" information (because it don’t
come from a file), I guess that the autosorting is kicking in. I think it
would be better if all the "autosorting" of the sublocations array inside
"Bio::Location::Split" were optional instead of automatic, because of these
cases.

Cheers,

Francisco J. Ossandon

-----Mensaje original-----
De: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] En nombre de Adam Witney
Enviado el: jueves, 08 de marzo de 2012 13:40
Para: bioperl-l at bioperl.org
Asunto: [Bioperl-l] Bio::Tools::Glimmer and genes wrapping around the origin

Hi,

I have been using Bio::Tools::Glimmer and have come across a problem with it
not handling genes that wraparound across the origin. I think I have boiled
it down to this test case of what happens internally with
Bio::Tools::Glimmer

##############################################################
#! /usr/local/bin/perl -w

use strict;
use warnings;

use Bio::Factory::FTLocationFactory;
use Bio::SeqFeature::Generic;

my $location_string = 'join(117..1,135690..135187)';

my $location_factory = Bio::Factory::FTLocationFactory->new();
my $location_object = $location_factory->from_string($location_string);

print "Location: ".$location_object->to_FTstring."\n";

my $gene = Bio::SeqFeature::Generic->new(
                 '-seq_id'      => 'Testing',
                 '-location'   => $location_object,
                 '-strand'     => -1
             );

print "Location: ".$location_object->to_FTstring."\n";

##############################################################

$ perl ../FTLocationTest.pl 
Location: complement(join(135187..135690,1..117))
Location: complement(join(1..117,135187..135690))

This happens because by setting the '-strand' in Bio::SeqFeature::Generic,
this calls the strand method in $location_object (Bio::Location::Split)
which then causes the problem (although I can't quite work out where...!

Is this intended behaviour?

Thanks

Adam
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