genomes_to_md5s

The routine genomes_to_md5s can be used to look up the MD5 value associated with each of a set of genomes. The MD5 values are computed when the genome is loaded, so this routine just retrieves the precomputed values.

Note that the MD5 value of a genome is independent of the contig names and case of the DNA sequences that make up the genome.

Example:

    genomes_to_md5s [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 genomes_to_md5s. It is documented as follows:

  $return = $obj->genomes_to_md5s($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 md5
genomes is a reference to a list where each element is a genome
genome is a string
md5 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.