[Bioperl-l] Re: Need help

[Lincoln Stein]

I believe that the gb_to_gff.pl script is old and doesn't create the correct 
version of GFF.  I will fix that and apologize to you for the inconvenience.

In the meantime, I recommend that you install the Genbank/EMBL proxy (see the 
instructions in the gbrowse INSTALL document).  You can then just type in 
NC_000117 into the gbrowser search box and it will populate the mysql 
database directly from GenBank.

For example, see here:

	http://www.wormbase.org/db/seq/gbrowse?name=NC_000117;source=embl

Lincoln

On Friday 21 March 2003 03:11 pm, Yu Pan wrote:
> Hi Sir,
>
> We are trying to build our own database (mysql) for chlamydia.
> I first down loaded the genome file NC_000117.gbk from NCBI site.
> Then I used the perl script gb_to_gff.pl from bioperl scripts libs. to
> convert the .gbk file to .gff file.
> Then I used the load_gff.pl tried to load the .gff file into the
> database.
> I got hundreds of  'duplicated id' and 'no fgroup id' error messages and
> no database created.
> If I use bulk_load_gff.pl, there is no error message, the database seems
> created fine.
> I check the database records, they looks fine. But when lanch the
> gbrowser, it won't work at all,
> there is no 'overview panel' or 'detail panel'.
>
> Please give me some instructions how to make it work. What's wrong in my
> procedure?
>
> Thanks.
>
> Yu Pan
>
>
>
>
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-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
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