[Bioperl-l] Bio::DB::GFF dna doesn't work

[Lincoln Stein]

Hi Philippe,

You now need to load the DNA directly into the mysql database using the 
--fasta option of the load script.  I hadn't intended to break the -fasta 
option, but apparently I did.

Lincoln

On Thursday 13 March 2003 12:28 pm, Philippe Vaglio wrote:
> Hi,
>
> After getting Bioperl1.2
> the following code using Bio::DB::GFF doesn't work any more
>
>
> use Bio::DB::GFF;
>
> my $db  = Bio::DB::GFF->new( -adaptor => 'dbi::mysqlopt',
>                                -dsn     => 'dbi:mysql:test',
>                                -fasta=>'fasta_files');
>
>
> my $segment = $db->segment('chr22',17900000,18000000);
>
> print $segment->dna;
>
>
> but does work with Bio::DB::GFF from bioperl 1.0.2
>
> Am I missing something ?

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
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