[ensembl-dev] slice fetch_all warnings

[Andy Yates]

Hi Hardip,

I believe this could have something to do with these sequences being marked as circular. The warnings are not a great concern (the logic still works as expected) but I will see what can be done about keeping them quiet.

Best regards,

Andy

On 12 Jul 2011, at 01:29, Hardip Patel wrote:

> Hi All
> 
> I am using the following code to obtain all toplevel slices for the yeast genome.
> 
> 
> my $slice_adaptor = $reg->get_adaptor('Saccharomyces cerevisiae', 'Core', 'Slice');
> foreach my $slice (@{$slice_adaptor->fetch_all('toplevel', 'EF3')}){
>   ...do something...
> }
> 
> However it is giving following warnings during the accession of Mito and 2-micro sequences.
> 
> Use of uninitialized value in numeric gt (>) at /short/sharedapps/Ensembl/ensembl63/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm line 150.
> 
> Could somebody please shed some light on these warnings and let me know if it is a minor glitch or something of big concern?
> 
> Thanking you
> 
> Kind regards
> 
> -- 
> Hardip R. Patel, PhD
> Bioinformatician, Molecular Genetics Division,
> Victor Chang Cardiac Research Institute,
> Darlinghurst, NSW – 2010, Australia
> (W): +61 – 2 – 9295 8611
> (M): 0449 180 715
> 
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-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/