How to run Mike Cherry's filtering script locally before checking the GAF into SVN?

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  • You need access to SVN to run the script locally. If you don't have access please write to go-admin@genome.stanford.edu
  • Familiarize yourself with SVN commands (http://geneontology.org/page/svn-help)
  • You need to check out the following files from SVN. The script will fail or will give you inaccurate reports if you don't have the current version of any of the files.

> svn --non-interactive --trust-server-cert --ignore-externals co svn+ssh://username@ext.geneontology.org/share/go/svn/trunk/ontology go/ontology
username@ext.geneontology.org's password:
[this will co the entire directory]

> svn --non-interactive --trust-server-cert --ignore-externals co svn+ssh://username@ext.geneontology.org/share/go/svn/trunk/gene-associations/submission go/gene-associations/submission
username@ext.geneontology.org's password:
[this will co the entire directory]

>svn --non-interactive --trust-server-cert --ignore-externals co svn+ssh://username@ext.geneontology.org/share/go/svn/trunk/software/utilities go/software/utilities
username@ext.geneontology.org's password:

> svn --non-interactive --trust-server-cert --ignore-externals co svn+ssh://username@ext.geneontology.org/share/go/svn/trunk/doc/ go/doc
username@ext.geneontology.org's password:

Now you have the necessary files to run the script in your space.

  • cd to the gene-associations/submission directory
 
>cd go/gene-associations/submission
 
>../../software/utilities/filter-gene-association.pl -e -i gene_association.sgd.gz

You should see the filtering script report once the script runs through the file.


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