NAME

Bio::Sketch::Mash

SYNOPSIS

A module to read `mash info` output and transform it

use strict;
use warnings;
use Bio::Sketch::Mash;

# Sketch all fastq files into one mash file.
# Mash sketching is not implemented in this module.
system("mash sketch *.fastq.gz > all.msh");
die if $?;

# Read the mash file.
my $msh = Bio::Sketch::Mash->new("all.msh");
# All-vs-all distances
my $distHash = $msh->dist($msh);

# Read a mash file, write it to a json-formatted file
my $msh2 = Bio::Sketch::Mash->new("all.msh");
$msh2->writeJson("all.json");
# Read the json file
my $mashJson = Bio::Sketch::Mash->new("all.json");
my $dist = $msh2->dist($mashJson); # yields a zero distance

DESCRIPTION

This is a module to read mash files produced by the Mash executable. For more information on Mash, see mash.readthedocs.org. This module is capable of reading mash files. Future versions will read/write mash files.

METHODS

Bio::Sketch::Mash->new("filename.msh",\%options);

Create a new instance of Bio::Sketch::Mash. One object per set of files.

Arguments:  Sketch filename (valid types/extensions are .msh, .json, .json.gz)
            Hash of options (none so far)
Returns:    Bio::Sketch::Mash object

$msh->loadMsh("filename.msh")

Changes which file is used in the object and updates internal object information. This method is ordinarily used internally only.

Arguments: One mash file
Returns:   self

$msh->loadJson("filename.msh")

Changes which file is used in the object and updates internal object information. This method is ordinarily used internally only.

Arguments: One JSON file describing a Mash sketch
Returns:   self

$msh->writeJson("filename.json")

Writes contents to a file in JSON format

Arguments: One filename
Returns:   self

$msh->dist($msh2)

Returns a hash describing distances between sketches represented by this object and another object. If there are multiple sketches per object, then all sketches in this object will be compared against all sketches in the other object.

Arguments: One Bio::Sketch::Mash object
Returns:   reference to a hash of hashes. Each value is a number.

Aliases: distance(), mashDist()

Bio::Sketch::Mash::raw_mash_distance($array1, $array2)

Returns the number of sketches in common and the total number of sketches between two lists. The return type is an array of two elements. This function is used internally with $msh->dist and assumes that the hashes are already sorted.

Arguments: A list of integers
           A list of integers
Returns:   (countOfInCommon, totalNumber)

Example:
  
  my $R1 = [1,2,3];
  my $R2 = [1,2,4];
  my($common, $total) = Bio::Sketch::Mash::raw_mash_distance($R1,$R2);
  # $common => 2
  # $total  => 3

$msh->fix()

Fixes a mash sketch if it is broken at all. For now this just sorts hashes but this subroutine could contain more fixes in the future.

Arguments: None
Returns:   $self

COPYRIGHT AND LICENSE

MIT license.

AUTHOR

Author: Lee Katz <lkatz@cdc.gov>

For additional help, go to https://github.com/lskatz/perl-mash

CPAN module at http://search.cpan.org/~lskatz/perl-mash