Re: [GMOD-devel] Another problem with gmod_bulk_load_gff3.pl

[Scott C. <cai...@gm...>]

Hi Dave,

I remember having a problem like this before, but I thought I'd fixed
it.  Apparently not :-/  I'll take a look.

Scott


On Mon, 2007-11-26 at 11:44 -0500, David Emmert wrote:
> Hey Scott,
> 
> I think I've found another bug in gmod_bulk_load_gff3.pl.
> 
> In loading .fasta files containing multiple fastas, it seems to be 
> always failing to load the first fasta file.  So for example in loading 
> Tribolium tca_ref_chrLG4.gbk.gff.sorted.fasta, which contains these 
> fastas:
> > NW_001092820
> > NW_001092818
> > NW_001092819
> > NW_001092816
> > NW_001092821
> > NW_001092822
> > NW_001092817
> the first record (NW_001092820) is skipped, while all the rest are 
> loaded.  I didn't see any indication of a problem in the output from 
> gmod_bulk_load_gff3.pl.   I've seen the same behavior in all of the data 
> I loaded for Tribolium and Apis.  Any idea whatup?
> 
> I'm going to send you a tarball of tca_ref_chrLG4 in a seperate mail to 
> use in debugging.  I'll take a shot at a workaround later today and let 
> you know if I figure anything out.
> 
> Best,
> 
> -Dave
> 
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Scott Cain, Ph. D.                                         ca...@cs...
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
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