svr_missing_roles -r reaction -g genome

It is assumed that -r is used to specify a column in the input file. The column should contain reaction IDs for which "missing roles" might exist. The -g argument is used to specify the column containing the genome ID.

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Example:

    svr_all_models | 
    svr_gap_filled_reactions_and_roles -c 2 | 
    cut -f1,2,3 | sort -u |
    svr_find_clusters_relevant_to_reaction -g 1 -c 3 |
    svr_find_hypos_for_cluster |
    svr_missing_roles -g 1 -r 3

would produce a 6-column table [Genome, Model, reaction, cluster-of-genes-connected-to-role, peg-for-hypothetical, PossibleRoles]

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Command-Line Options

-r ReactionColmun

Specifies which column in the input table contains the reaction ID.

-g GenomeColumn

Specifies which column in the input contains the genome ID, or it can give the actual genome ID, if you are processing a single genome.

Output Format

The standard output is a tab-delimited file. Each line will contain the input fields followed by one or more new columns, each containing a functional role that appears to be missing (and, hence, a candidate for a hypothetical).