[Bioperl-l] weird behavior with bulk_load_gff

Michael Eisen mbeisen at lbl.gov
Sat Dec 18 21:56:12 EST 2004

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?

Michael B. Eisen, Ph.D. (MBEISEN at LBL.GOV)

Genome Sciences Division, Lawrence Berkeley Natl Lab
Dept. of Molecular and Cell Biology, UC Berkeley

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