NAME

go-prepare-release.pl

SYNOPSIS

go-prepare-release.pl -f mygo.conf 

DESCRIPTION

Builds a GO database from various flat file components

It will build 4 databases in order, each database subsumes the previous one. Two mysqldumps will be generated for each db

PRERQUISITES

You need both go-perl and go-db-perl installed

DATABASES CONSTRUCTED

termdb

A db containing only the ontology

required files:

$GO/ontology/*.ontology
$GO/ontology/GO.defs
$GO/ontology/external2go/*

A CVS update will be performed to get the correct files for the release

extra files generated:

rdf-xml
coderelease

assocdb

A db subsuming termdb that contains the gene associations

required files:

$GO/gene-associations/*

seqdb

A db subsuming assocdb that includes some sequence data

required files:

$GO/gp2protein/*
./proteomes/*SPC

The proteomes dir is automatically downloaded from EBI

ftp://ftp.ebi.ac.uk/pub/databases/SPproteomes/swissprot_files/proteomes

seqdblite

The same as seqdb but with the IEA associations removed

extra files generated:

fasta
rdf-xml

ARGUMENTS

-f CONFFILE

-i

interactive mode

-monthly

make a monthly release

will cvs check out from the 1st of the month and build a release corresponding to that date

-daily

make a daily release

SEE ALSO