roles_to_fids

You often wish to find the fids in one or more genomes that
implement specific functional roles.  To do this, you can use
roles_to_fids.

Example:

roles_to_fids [arguments] < input > output

The standard input should be a tab-separated table (i.e., each line is a tab-separated set of fields). Normally, the last field in each line would contain the identifer. If another column contains the identifier use

-c N

where N is the column (from 1) that contains the subsystem.

This is a pipe command. The input is taken from the standard input, and the output is to the standard output.

Documentation for underlying call

This script is a wrapper for the CDMI-API call roles_to_fids. It is documented as follows:

$return = $obj->roles_to_fids($roles, $genomes)

Parameter and return types

$roles is a roles
$genomes is a genomes
$return is a reference to a hash where the key is a role and the value is a fid
roles is a reference to a list where each element is a role
role is a string
genomes is a reference to a list where each element is a genome
genome is a string
fid is a string

Command-Line Options

-c Column

This is used only if the column containing the subsystem is not the last column.

-i InputFile [ use InputFile, rather than stdin ]

genomes - A list of genomes to restricty the output

Output Format

The standard output is a tab-delimited file. It consists of the input file with extra columns added.

Input lines that cannot be extended are written to stderr.