This directory contains scripts for producing GO slim annotations for EST and other data.

run_goslim is the main script that calls other scripts to parse data and then calls map2slim.pl (obtained from geneontology.org) to produce the mappings. The mappings are then counted and a tab delimited file output.

Note: map2slim.pl requires a local installation of the GO database. It can be obtained on www.geneontology.org.

Another Note: the convert2tab.pl can take a -c switch. In that case it will produce gene counts that are normalized for the number of annotations per gene (The sum of all the genes in the GO slim should add up to the total number of genes input). If -c is omitted, a full annotation (that +1) will be added to each go slim category. Because genes can be annotated to different categories, the counts of annotations in the go slim will be larger than the number of genes.

Lukas, Feb 24, 2005

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Jane, stop this crazy thing!
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Super quick-and-dirty unWTF...

	0. Download GO mysql database (if applicable)
		from: http://www.godatabase.org/dev/database/archive/latest/
		file: go_<YYYY-MM>-termdb-tables.tar.gz
		commands:
			# tar -zxvf go_<YYYY-MM>-termdb--tables.gz
			# cd <releasedir>
			# echo "create database go" | mysql -p
			# cat *.sql | mysql -p mygo
			# mysqlimport -p -L mygo *.txt

	1. Install necessary perl modules (if applicable)
		install C/CM/CMUNGALL/go-perl-0.01.tar.gz		
		download go-dev package:
			http://sourceforge.net/project/showfiles.php?group_id=36855&package_id=33201
			cd into the go-db-perl directory that tarball contains
				perl Makefile.pl
				make
				make install

	2. edit run_goslim.sh file to have YOUR db username/password

	3. Get other required go files:
		AT_go_assoc_file: (GO assocation file from TAIR)
			from: ftp://ftp.arabidopsis.org/home/tair/Ontologies/Gene_Ontology/
			e.g.: ATH_GO_GOSLIM.20050219.txt
		go_slim_file: (A file with the go slim definitions)
			from: ftp://ftp.geneontology.org/pub/go/GO_slims/
			e.g.: goslim_generic.go

	4. Obtain blast result file in the necessary format (-m8 output?)
		For FGN/PGN formatted blast results files, use the
		parse_teri_blast.pl script:
			# ./parse_teri_blast.pl <in.txt >out.txt

	5. Use the run_goslim wrapper script.  Debug as required.
			# ./run_goslim.sh AT_parsed_blast_results AT_go_assoc_file go_slim_file
			e.g.,
				./run_goslim.sh ste02_go_source.txt ATH_GO_GOSLIM.20050219.txt goslim_generic.go
