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
  • Familiarize yourself with SVN commands (
  • 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:// go/ontology's password:
[this will co the entire directory]

> svn --non-interactive --trust-server-cert --ignore-externals co svn+ssh:// go/gene-associations/submission's password:
[this will co the entire directory]

>svn --non-interactive --trust-server-cert --ignore-externals co svn+ssh:// go/software/utilities's password:

> svn --non-interactive --trust-server-cert --ignore-externals co svn+ssh:// go/doc'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/ -e -i gene_association.sgd.gz

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

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