protein_families_to_fids

protein_families_to_fids can be used to access the set of fids represented by each of a set of protein_families. We define protein_families as sets of fids (rather than sets of MD5s. This may, or may not, be a mistake.

Example:

protein_families_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. For each input line, there are multiple output lines, one for each fid in the family, the fid is added to the end of each output line.

Documentation for underlying call

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

$return = $obj->protein_families_to_fids($protein_families)

Parameter and return types

$protein_families is a protein_families
$return is a reference to a hash where the key is a protein_family and the value is a fids
protein_families is a reference to a list where each element is a protein_family
protein_family is a string
fids is a reference to a list where each element is a fid
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 ]

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.