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

[Fields, Christopher J]

I agree, no sorting should be implied (a 'join' order should be based on order of addition alone, and sort should be optional).  IIRC there were backwards-compat problems switching this due to reliance on old behavior, but it might be worth trying to see if anything breaks test-wise (and why it breaks).

chris

On Mar 8, 2012, at 2:37 PM, Francisco J. Ossandón wrote:

> 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
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l