[Bioperl-l] Re: BioPerl GFF scripts

[Lincoln Stein]

Hi Marc,

Apparently the bioperl build process still doesn't install the scripts (any of 
them) but leaves them in the build directory.  You will have to copy them 
manually from scripts/Bio-DB-GFF into /usr/local/bin.  This will be fixed in 
the next release.

I will add a note about fast_load_gff.pl to the perldoc.  I'm still not sure 
whether it is fully general  -- it uses a lot of pipe tricks that might only 
work with certain Unix flavors.

the load_gff.pl script will actually work with any Bio::DB::GFF adaptor; you 
specify the adaptor with --adaptor.  The bulk and fast loaders invoke the 
mysql interactie shell directly -- that's why they're fast.  If you want to 
use biosql, then you should use the biosql loader application.  Gbrowse will 
run on top of biosql, but the biosql API is completely different from 
Bio::DB::GFF.

If you're interested in doing the Postgres port of Bio::DB::GFF I will gladly 
offer you assistance and accolades.

Lincoln

On Friday 14 March 2003 06:42 pm, Marc Colosimo wrote:
> Lincoln,
>
> Sorry for being a pain, but after installing the newest BioPerl (had to
> find the new libgd) I looked at the perldoc for Bio::DB::GFF. It said
> that there should be several scripts (load_gff.pl, etc...), however,
> they are no where to be found with in installed module. I did find them
> where I built bioperl. I don't know if you want to fix this so that they
> get installed with Bio. Also, I see you added another script
> fast_load_gff.pl, which is not in the perldoc
>
> I noticed that for load_gff scripts that they will only load into a
> MySQL database. Is that because you have not written an adaptor for
> others and do these use the biosql database for a backend?
>
> I am interested in using a postgre database and would be interested in
> adding code for it. I want a database with affymetrix array stuff and
> worm genes for quick access. I also know that Craig Hunter is looking
> into getting their annotations onto wormbase.
>
> Marc

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
	1 Bungtown Road, Cold Spring Harbor, NY 11724
========================================================================