[Bioperl-l] load_gff.pl question

[Lincoln Stein]

I know it is very late to be answering this (I was on vacation in the month of 
August) but the problem is the database schema, which has a uniqueness 
constraint on features.  To be considered unique, a feature must have a 
unique combination of seq_id,start,end,feature_type and name.  If you are 
trying to load several features that have the same position and type, then 
try giving each of them a different name in order to differentiate them.  
Alternatively, you could go into the database and redefine this constraint.

Lincoln

On Tuesday 05 August 2003 05:17 pm, Shin Enomoto wrote:
> I am getting erratic results with the load_gff.pl.
>
> 1) I was trying to load a table of 900 lines. Of the 900 entries,  ~30
> are highly unique and they all loaded normally. The remainder was ~600,
>   ~250 and 4 of very similar items only differing slightly. It loaded
> 6/600, 5/250 and 2/4.
>
> 2) I have 10 large tables of ~250000 lines each. I was able to load the
> first table. load_gff.pl will not load any other tables.
>
> Where do I start to customize this script to allow loading of large
> number of similar entities?
>
>
>
>
> Shin Enomoto
> 295 ASLVM
> 1988 Fitch Ave.
> St. Paul, MN 55108
>
> 612-625-7737
>
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-- 
Lincoln Stein
lstein at cshl.edu
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)