[Bioperl-l] weird behavior with bulk_load_gff

[Allen Day]

have you tried using bioperl-live HEAD ?  if so, did the problem go away?

-allen

On Sat, 18 Dec 2004, Allen Day wrote:

> are you using bioperl-live HEAD, a bioperl-live tag/branch, or a bioperl
> release?
> 
> what is the error message, if any?
> 
> -allen
> 
> 
> On Sat, 18 Dec 2004, Michael Eisen wrote:
> 
> > I am having a very frustrating time loading a gff database and 
> > associated fasta files. This is something I've done thousands of times 
> > before, but for some reason, it's choking on my latest set of files, and 
> > I can't figure out why.
> > 
> > The files are contigs and scaffolds from an assembly of a fly genome. 
> > I've got a fasta file with the scaffolds (17 of them), and an associated 
> > gff file.
> > 
> > bulk_load_gff runs fine, all of the gff records are loaded into the 
> > fdata, but only loading 6 of the 17 sequences are loaded
> > 
> > when I try to run it splitting the scaffolds into individual files, it 
> > again only loads 6 of them, but this time a different 6 (in each case it 
> > only loads the first 6 - from a file the first six in the file, from a 
> > directory the first six in lexigraphic order)
> > 
> > Any thoughts on what's going wrong?
> > 
> > 
> > 
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