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

[Philip E Macmenamin]

Hi, 

In all other copies of wormbase the fref part of the fdna table has the chromosome as: I ... X. The fref for wormbase115 is Chromosome_I ... Chromosom_X. When the GFF program asks for dna it passes the chromosome ref as just I or X, and not finding anything. This could be fixed in the db by changing the entries in the fdna table. Or by changing the orig sequence files back to the previous Wormbase format (ie I, II, III, etc). Or by tricking around with Lincoln's load_gff script. 

Philip. 


----- Original Message -----
From: Lincoln Stein <lstein at cshl.edu>
Date: Friday, December 12, 2003 4:12 pm
Subject: Re: [Bioperl-l] Bio::DB::GFF dna method not working for wormbase115.

> 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.
>