[Bioperl-l] end < start?

[Estienne Swart]

  Hi All,

I'm not quite sure who I should be directing this email too (possibly 
the transcript module maintainer? Ensembl dev mailing list?), but hope 
that someone will be able to address my problem.

When trying to retrieve translateable portions of transcripts (from 
human chr22) using the following (in a standard SliceAdaptor based script):

foreach my $transcript (@$transcripts){
            print ">" . $transcript->stable_id . "\n" . 
$transcript->translateable_seq() . "\n";

I was able to obtain a few sequences, before the following error message 
was returned:


    -------------------- EXCEPTION --------------------
    MSG: End coord is less then start coord
    STACK Bio::EnsEMBL::Slice::subseq
    /usr/lib/perl5/5.6.1/Bio/EnsEMBL/Slice.pm:307
    STACK Bio::EnsEMBL::Exon::seq
    /usr/lib/perl5/5.6.1/Bio/EnsEMBL/Exon.pm:1593
    STACK Bio::EnsEMBL::Transcript::translateable_seq
    /usr/lib/perl5/5.6.1/Bio/EnsEMBL/Transcript.pm:396
    STACK toplevel /mnt/hdb6/progs/fetch_ensembl_cds.pl:40
    -------------------------------------------


As far as I can tell, the transcript module should not receive 
sequences, where start > end (on the reverse strand?).

Does anyone know what's going on here?

I could figure this out myself, but I'm afraid that this might be rather 
time consuming, and it looks like there may be quite a few dependencies 
that I'll have to try to resolve.


Cheers

Estienne

-- 
Estienne Swart
SANBI, UWC Private Bag X17, Bellville 7535
estienne@sanbi.ac.za
tel work: +27 21 959 3908
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