p3-co-occur

Compute Co-Occurrences of Proteins

p3-co-occur.pl [options] catFile

This script will compute the number of co-occurrences of specified protein categories. The most common category is role (product), but it is also possible to specify protein families.

Parameters

The positional parameter is the name of the file containing the category names. The file should be tab-delimited with the names in the first column. If no file is specified, all recognizable category values will be counted. This can be problematic if the categories are roles.

The standard input can be overridden using the options in Input Options. The standard input will contain the genome IDs. The options in Column Options can be used to configure headers and the column containing the genome IDs. In addition, the following options are supported.

• gap

The maximum gap distance for two proteins to be considered physically close. The default is 2000.

• type

The type of category– currently role, ecnum, or family. The default is role.

• verbose

If specified, status messages will be written to the standard error output.