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

[Adam Witney]

Thanks for your replies.

After a little more digging there seems to be two things. In the test code i posted, the extra strand attribute in Bio::SeqFeature::Generic (and subsequent call to location_object->strand) changes the internal guide_strand such that this line in Bio::Location::Split->to_FTstring changes the order of subLocations:

	my @locs = ($stype eq 'join' && (!$guide && $strand == -1)) ?
	           reverse $self->sub_Location() : $self->sub_Location() ;

The second problem is probably due to the sorting order within Bio::SeqFeature::Generic when calling 'start' and 'end' then it doesn't do the right thing in this case. But I am not quite sure how to fix this.

Thanks again

Adam

On 8 Mar 2012, at 21:38, Fields, Christopher J wrote:

> 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
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>> 
>> 
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