NAME

Mash

SYNOPSIS

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

  use strict;
  use warnings;
  use 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 = 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 = Mash->new("all.msh");
  $msh2->writeJson("all.json");
  # Read the json file
  my $mashJson = 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

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

Create a new instance of 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:    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 Mash object
  Returns:   reference to a hash of hashes. Each value is a number.

Aliases: distance(), mashDist()

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, $total) = Mash::raw_mash_distance($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