proteins_to_fids

proteins_to_fids takes as input a list of proteins (i.e., a list of md5s) and returns for each a set of protein-encoding fids that have the designated sequence as their translation. That is, for each sequence, the returned fids will be the entire set (within Kbase) that have the sequence as a translation.

Example:

proteins_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 the protein maps to. The fid is added to the end of each line.

Documentation for underlying call

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

$return = $obj->proteins_to_fids($proteins)

Parameter and return types

$proteins is a proteins
$return is a reference to a hash where the key is a protein and the value is a fids
proteins is a reference to a list where each element is a protein
protein 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.