WormBase gene association file

Generating the WormBase gene association file

In the acedb user account on Tazendra at:/home/acedb/ranjana/GO:

1. Use ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS211/ONTOLOGY/ eg., to get the latest gene association file generated by WormBase EBI eg., gene_association.WS211.wb.ce.
2. Use 'grep IEA gene_association.WSXXX.wb.ce > gene_association.wb.electronic to separate the IEAs.
3. Grep WBPhenotype gene_association.WSXXX.wb.ce > gene_association.wb.rnai2go(to get i.e both Erich's earlier RNAi2GO ones and the new associations based on allele phenotypes that went into WormBase WS186).
4. copy the right go.go.<date> file from /home/acedb/ranjana/citace_upload/go_curation/go_dumper_files/ to this directory,change name to gene_association.wb.manual.
5. Cd to the /external_annots directory and download a new GOA elegans file, from 04.02.12, for external annots (use 'wget ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/9.C_elegans.goa')
6. Run the ./wrapper.pl script, note this script generates both go.ace and go.go (gene association format file) in the go_dumper_files directory:
7. ./wrapper.pl gives the following output:

filtering secondary GO IDs into .no_secondary filenames now and outputs NUMBER of ERRORS by COLUMN:

1. Run strip_errors_and_concatenate.pl, this script also generates gene, GO term numbers.