[Bioperl-l] weird behavior with bulk_load_gff

Allen Day allenday at ucla.edu
Sat Dec 18 23:31:20 EST 2004

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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