Chris Mungall > go-db-perl-0.01 > go-prepare-release.pl

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Source   Latest Release: go-db-perl-0.04

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 ^

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