md5s_to_genomes

md5s to genomes is used to get the genomes associated with each of a list of input md5 values.

The routine takes as input a list of MD5 values.  It constructs a mapping from each input
MD5 value to a list of genomes that share the same MD5 value.

The MD5 value for a genome is independent of the names of contigs and the case of the DNA sequence
data.

Example:

md5s_to_genomes [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 md5s_to_genomes. It is documented as follows:

$return = $obj->md5s_to_genomes($md5s)

Parameter and return types

$md5s is a md5s
$return is a reference to a hash where the key is a md5 and the value is a genomes
md5s is a reference to a list where each element is a md5
md5 is a string
genomes is a reference to a list where each element is a genome
genome 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.