svr_discriminating_functions

    svr_discriminating_functions genome_ids1.tbl genome_ids2.tbl >role_list.tbl

Analyze two groups of genomes and return a list of the functions that discriminate between them.

A function discriminates between two groups of genomes if it is common in one and uncommon in the other.

This script takes as input two tab-delimited files with genome IDs at the end of each line. It writes out a single tab-delimited file with four columns.

Alternatively, the script can be used as a pipe command. If no positional parameters are specified, the first group will be taken from the standard input.

If no second group is specified, then the second group will be all complete genomes not in the first group. Optionally, it can be all prokaryotic complete genomes not in the first group.

1. The FIGfam ID of a function.
2. The function of the identified FIGfam.
3. A score indicating the degree of discrimination. A score of 2 indicates the function occurs universally in one group and not at all in the other. All scores will be greater than 1
4. 1 if the function tends to be in the first group and 2 if it tends to be in the second.

The output will be sorted by the fourth column, so the results will be presented with the roles discriminating in favor of the first group followed by the roles discriminating in favor of the second group.

Command-Line Options

url

The URL for the Sapling server, if it is to be different from the default.

c

Column index. If specified, indicates that the input IDs should be taken from the indicated column instead of the last column. The first column is column 1. This parameter applies to both input files.

prok

If specified, and if no second group is present, the second group will be limited to prokaryotic genomes.