Difference between revisions of "WormBase gene association file"
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====Generating the WormBase gene association file==== | ====Generating the WormBase gene association file==== | ||
In the acedb user account on Tazendra at:/home/acedb/ranjana/GO: | In the acedb user account on Tazendra at:/home/acedb/ranjana/GO: | ||
− | #Use ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS211/ONTOLOGY/ | + | #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. |
#Use 'grep IEA gene_association.WSXXX.wb.ce > gene_association.wb.electronic to separate the IEAs. | #Use 'grep IEA gene_association.WSXXX.wb.ce > gene_association.wb.electronic to separate the IEAs. | ||
#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). | #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). | ||
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#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: | #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: | ||
#./wrapper.pl gives the following output: | #./wrapper.pl gives the following output: | ||
− | filtering secondary GO IDs into .no_secondary filenames now | + | filtering secondary GO IDs into .no_secondary filenames now and outputs NUMBER of ERRORS by COLUMN: |
− | + | #Run strip_errors_and_concatenate.pl, this script also generates gene, GO term numbers. | |
− | |||
− | |||
− | and outputs NUMBER of ERRORS by COLUMN |
Revision as of 18:03, 23 October 2012
Generating the WormBase gene association file
In the acedb user account on Tazendra at:/home/acedb/ranjana/GO:
- 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.
- Use 'grep IEA gene_association.WSXXX.wb.ce > gene_association.wb.electronic to separate the IEAs.
- 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).
- 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.
- 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')
- 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:
- ./wrapper.pl gives the following output:
filtering secondary GO IDs into .no_secondary filenames now and outputs NUMBER of ERRORS by COLUMN:
- Run strip_errors_and_concatenate.pl, this script also generates gene, GO term numbers.