[Bioperl-l] Bio::DB::GFF dna method not working for wormbase115.

[Lincoln Stein]

It's working OK with me on Wormbase 115.  One issue is that DNA is 
numbered from 1 onward, not from 0.

Lincoln

On Wednesday 10 December 2003 01:24 pm, Philip MacMenamin wrote:
> Hi,
> I have just loaded wormbase fatsa files to a GFF SQL database using
> Lincolns load_gff script, and everything was fine.
>
> However when I try to get the dna back out, using the same script
> that worked (works) for wormbase110 does not work now, ie:
>
> use Bio::DB::GFF;
> doConection stuff blah blah blah;
> my $segment1 = $db->segment('I',0, 2000);
> my $dna = $segment1->dna;
> print $dna if $debug;
>
> I can step through the perl debugger and find out how the story is
> differant between version 110 and 115, but at first look the
> databases seem similar.
>
> I looked through the mail archives to see if others have had this
> problem, but drew a blank, so I want to make sure that this is
> known.
>
> All the best,
> Philip.