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− | ====Old SOP for generating a .ace file for GO data====
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− | ====Old SOP for generating a gene association file====
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− | In the acedb user account on Tazendra at:/home/acedb/ranjana/GO:
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− | --Use ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS211/ONTOLOGY/gene_association.WS211.wb.ce
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− | --use'grep IEA gene_association.WSXXX.wb.ce>gene_association.wb.electronic to separate the IEAs.
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− | --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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− | --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.
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− | --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')
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− | --Run the ./wrapper.pl script
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− | Output will include the various error types
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− | --Run ./strip_errors_and_concatenate.pl
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− | Scp the generated gene association file to a local machine for post-processing and upload to the GOC In the tmp directory on Maya: --scp file to Maya
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− | --removed 'NOT' annotations from mtm-9, vha-2, vha-3, hsp-60, hsp-12.3, hsp-12.6. (We do not take out NOT annotations anymore)
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− | --removed header from the middle of concatenated file in two places (on top of UniProt file too, search for 'gaf-version') and placed on top of file (correct minor mistake in header--space after the $ on one of the lines)
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− | --And move the following header from the middle of file to the top of file:
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− | !Version: $Revision: $
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− | !Organism: Caenorhabditis elegans
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− | !date: $Date: $
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− | !From: WormBase
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− | --Add these two lines at the bottom of header:
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− | !DataBase_Project_Name: WormBase WS215/WS216
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− | !gaf-version: 2.0
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− | --Remove the header 'gaf 2.0', from the top of the UniProt file
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− | --gzip file
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− | --Copy file to the tmp directory
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− | Use SVN commands to upload to the GO, also update README file every upload.
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