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NAME

Bio::Kmer - Helper module for Kmer Analysis.

SYNOPSIS

A module for helping with kmer analysis.

use strict;
use warnings;
use Bio::Kmer;

my $kmer=Bio::Kmer->new("file.fastq.gz",{kmercounter=>"jellyfish",numcpus=>4});
my $kmerHash=$kmer->kmers();
my $countOfCounts=$kmer->histogram();

my $minimizers = $kmer->minimizers();
my $minimizerCluster = $kmer->minimizerCluster();

The BioPerl way

use strict;
use warnings;
use Bio::SeqIO;
use Bio::Kmer;

# Load up any Bio::SeqIO object. Quality values will be
# faked internally to help with compatibility even if
# a fastq file is given.
my $seqin = Bio::SeqIO->new(-file=>"input.fasta");
my $kmer=Bio::Kmer->new($seqin);
my $kmerHash=$kmer->kmers();
my $countOfCounts=$kmer->histogram();

DESCRIPTION

A module for helping with kmer analysis. The basic methods help count kmers and can produce a count of counts. Currently this module only supports fastq format. Although this module can count kmers with pure perl, it is recommended to give the option for a different kmer counter such as Jellyfish.

DEPENDENCIES

* BioPerl
* Jellyfish >=2
* Perl threads
* Perl >=5.10

VARIABLES

$Bio::Kmer::iThreads

Boolean describing whether the module instance is using threads

METHODS

Bio::Kmer->new($filename, \%options)

Create a new instance of the kmer counter. One object per file.

Filename can be either a file path or a Bio::SeqIO object.

Applicable arguments for \%options:
Argument     Default    Description
kmercounter  perl       What kmer counter software to use.
                        Choices: Perl, Jellyfish.
kmerlength|k 21         Kmer length
numcpus      1          This module uses perl 
                        multithreading with pure perl or 
                        can supply this option to other 
                        software like jellyfish.
gt           1          If the count of kmers is fewer 
                        than this, ignore the kmer. This 
                        might help speed analysis if you 
                        do not care about low-count kmers.
sample       1          Retain only a percentage of kmers.
                        1 is 100%; 0 is 0%
                        Only works with the perl kmer counter.
verbose      0          Print more messages.

Examples:
my $kmer=Bio::Kmer->new("file.fastq.gz",{kmercounter=>"jellyfish",numcpus=>4});
$kmer->ntcount()

Returns the number of base pairs counted. In some cases such as when counting with Jellyfish, that number is not calculated; instead the length is calculated by the total length of kmers. Internally, this number is stored as $kmer->{_ntcount}.

Note: internally runs $kmer->histogram() if $kmer->{_ntcount} is not initially found.

Arguments: None
Returns:   integer
$kmer->count()

Count kmers. This method is called as soon as new() is called and so you should never have to run this method. Internally caches the kmer counts to ram.

Arguments: None
Returns:   None
$kmer->clearCache

Clears kmer counts and histogram counts. You should probably never use this method.

Arguments: None
Returns:   None
$kmer->query($queryString)

Query the set of kmers with your own query

Arguments: query (string)
Returns:   Count of kmers. 
            0 indicates that the kmer was not found.
           -1 indicates an invalid kmer (e.g., invalid length)
$kmer->histogram()

Count the frequency of kmers. Internally caches the histogram to ram.

Arguments: none
Returns:   Reference to an array of counts. The index of 
           the array is the frequency.
$kmer->kmers

Return actual kmers

Arguments: None
Returns:   Reference to a hash of kmers and their counts
$kmer->minimizers(5)

Finds minimizer of each kmer

Arguments: length of minimizer (default: 5)
returns: hash ref, e.g., $hash = {AAAAA=>AAA, TAGGGT=>AGG,...}
$kmer->minimizerCluster(5)

Finds minimizer of each kmer

Arguments: length of minimizer (default: 5). 
  Internally, calls $kmer->minimizer($l) 
  If $kmer->minimizer has already been called, this parameter will be ignored.
returns: hash ref, e.g., $hash = {AAA=>[TAAAT, AAAGG,...], ATT=>[GATTC,...]}}
$kmer->union($kmer2)

Finds the union between two sets of kmers

Arguments: Another Bio::Kmer object
Returns:   List of kmers
$kmer->intersection($kmer2)

Finds the intersection between two sets of kmers

Arguments: Another Bio::Kmer object
Returns:   List of kmers
$kmer->subtract($kmer2)

Finds the set of kmers unique to this Bio::Kmer object.

Arguments: Another Bio::Kmer object
Returns:   List of kmers
$kmer->close()

Cleans the temporary directory and removes this object from RAM. Good for when you might be counting kmers for many things but want to keep your overhead low.

Arguments: None
Returns:   1

COPYRIGHT AND LICENSE

MIT license. Go nuts.

AUTHOR

Author: Lee Katz <lkatz@cdc.gov>

For additional help, go to https://github.com/lskatz/Bio--Kmer

CPAN module at http://search.cpan.org/~lskatz/Bio-Kmer/