genomes_to_fids

genomes_to_fids is used to get the fids included in specific genomes. It is often the case that you want just one or two types of fids -- hence, the types_of_fids argument.

Example:

genomes_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, ther can be many output lines, one per feature. The feature id is added to the end of the line.

Documentation for underlying call

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

$return = $obj->genomes_to_fids($genomes, $types_of_fids)

Parameter and return types

$genomes is a genomes
$types_of_fids is a types_of_fids
$return is a reference to a hash where the key is a genome and the value is a fids
genomes is a reference to a list where each element is a genome
genome is a string
types_of_fids is a reference to a list where each element is a type_of_fid
type_of_fid 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 ]

type

This is the type of the fid requested, i.e. peg, rna, etc.

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.