fids_to_protein_families

Kbase supports the creation and maintence of protein families. Each family is intended to contain a set of isofunctional homologs. Currently, the families are collections of translations of features, rather than of just protein sequences (represented by md5s, for example). fids_to_protein_families supports access to the features that have been grouped into a family. Ideally, each feature in a family would have the same assigned function. This is not always true, but probably should be.

Example:

    fids_to_protein_families [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 fids_to_protein_families. It is documented as follows:

  $return = $obj->fids_to_protein_families($fids)

Parameter and return types

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