[ensembl-dev] Script from variation api tutorial throwing exceptions

[Will McLaren]

Hi Daniel,

You've unearthed a bug in the API - please update from CVS your
ensembl-variation API module to get this working.

Thanks

Will McLaren
Ensembl Variation

On 19 July 2012 12:44, Daniel Cuevas <cuevaszd at cs.man.ac.uk> wrote:
>
> Hi to all,
>
> I am trying to print the flanking sequences from a set of SNPs, so I've
> found this script in the variation API tutorial. However, it is throwing the
> following exception when I execute it:
>
> -------------------- EXCEPTION --------------------
> MSG: End coord + 1 is less than start coord
> STACK Bio::EnsEMBL::Slice::subseq ensembl/modules/Bio/EnsEMBL/Slice.pm:632
> STACK Bio::EnsEMBL::Variation::DBSQL::VariationAdaptor::_get_flank_from_core
> ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VariationAdaptor.pm:1395
> STACK
> Bio::EnsEMBL::Variation::DBSQL::VariationAdaptor::get_flanking_sequence
> ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VariationAdaptor.pm:1024
> STACK Bio::EnsEMBL::Variation::Variation::five_prime_flanking_seq
> ensembl-variation/modules/Bio/EnsEMBL/Variation/Variation.pm:768
> STACK main::get_VariationFeatures bioperl_test4.pl:34
> STACK toplevel bioperl_test4.pl:24
> Ensembl API version = 67
>
> I've attached the script to this e-mail. Could you please help me to find
> the problem?
>
> Thank you in advance,
> Daniel
>
>
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