genomes_to_contigs

The routine genomes_to_contigs can be used to retrieve the IDs of the contigs associated with each of a list of input genomes. The routine constructs a mapping from genome ID to the list of contigs included in the genome.

Example:

    genomes_to_contigs [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 line of input, there can be multiple output lines, one per contig. The contig id is added to the end of each line.

Documentation for underlying call

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

  $return = $obj->genomes_to_contigs($genomes)

Parameter and return types

$genomes is a genomes
$return is a reference to a hash where the key is a genome and the value is a contigs
genomes is a reference to a list where each element is a genome
genome is a string
contigs is a reference to a list where each element is a contig
contig 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.