Re: [GMOD-devel] chado db to bulk feature,sequence files package

[Scott C. <ca...@cs...>]

Hi Don,

Thanks for this--I don't think it will make it into the current release
I am planning (which should be out soon), but I will take a look at it
some time this week.

Scott


On Mon, 2004-08-23 at 04:12, Don Gilbert wrote:
> Dear folks,
> 
> I've added a Perl package to gmod/schema/GMODTools/ which has most of the
> parts we are using in flybase now to create bulk sequence, feature files
> for public distribution.  Some further work is still needed, but it
> can be used as-is.  Comments, suggestions, improvements are welcome.
> 
>   Bio::GMOD::Bulkfiles -- produce bulk sequence and feature files
>     from Chado genome database for public distribution .
>   
>   This generates Fasta, GFF v3, DNA and other bulk genome annotation files at
>     ftp://flybase.net/genomes/Drosophila_melanogaster/current/
>   It is tested with Flybase chado dbs, and SGD Lite chado db
>   
>   Bulkfiles is mostly self-contained, but uses a few BioPerl parts, 
>   Bio::GMOD::Config, XML::Simple for configuration files.  All of the
>   organism/database-specific logic should be in configuration files 
>   (schema/GMODTools/conf/)
> 
>   Find source here (sometime soon)
>   set cvsd=':pserver:ano...@cv...:/cvsroot/gmod'
>   cvs -d $cvsd login ; cvs -d $cvsd co schema/GMODTools
> 
> QUICK TEST :
> 
>   # get soft
>   cvs -d $cvsd co -d GMODTools schema/GMODTools
>   
>   # load a chado db to Postgres
>   wget http://sgdlite.princeton.edu/download/sgdlite/2004_05_19_sgdlite.sql.gz
>   createdb sgdlite_20040519
>   (zcat *sgdlite.sql.gz | psql -d sgdlite_20040519 -f - ) >& log.load 
>   
>   # replace root path in configs
>   perl -pi.old -e 's,\${ARGOS_ROOT}/flybase,$ENV{PWD},'   GMODTools/conf/*.xml
>   perl -pi.old -e 's,ARGOS_ROOT=.*,ARGOS_ROOT=$ENV{PWD},' GMODTools/conf/gmod.conf
>   
>   # run with sample config
>   perl -I./GMODTools/lib/ GMODTools/bin/bulkfiles.pl sgdbulk1
> 
> -- Don
> -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
> -- gil...@in...--http://marmot.bio.indiana.edu/
> 
> 
> -------------------------------------------------------
> SF.Net email is sponsored by Shop4tech.com-Lowest price on Blank Media
> 100pk Sonic DVD-R 4x for only $29 -100pk Sonic DVD+R for only $33
> Save 50% off Retail on Ink & Toner - Free Shipping and Free Gift.
> http://www.shop4tech.com/z/Inkjet_Cartridges/9_108_r285
> _______________________________________________
> Gmod-devel mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-devel
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         ca...@cs...
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory