[Bioperl-l] weird behavior with bulk_load_gff
allenday at ucla.edu
Mon Dec 20 21:34:25 EST 2004
have you tried using bioperl-live HEAD ? if so, did the problem go away?
On Sat, 18 Dec 2004, Allen Day wrote:
> are you using bioperl-live HEAD, a bioperl-live tag/branch, or a bioperl
> what is the error message, if any?
> 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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