Grinder::KmerCollection(3) A collection of kmers from sequences

SYNOPSIS


my $col = Grinder::KmerCollection->new( -k => 10,
-file => 'seqs.fa' );

DESCRIPTION

Manage a collection of kmers found in various sequences. Store information about what sequence a kmer was found in and its starting position on the sequence.

AUTHOR

Florent Angly <[email protected]>

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 Title   : new
 Usage   : my $col = Grinder::KmerCollection->new( -k => 10, -file => 'seqs.fa', -revcom => 1 );
 Function: Build a new kmer collection
 Args    : -k        set the kmer length (default: 10 bp)
           -revcom   count kmers before and after reverse-complementing sequences
                     (default: 0)
           -seqs     count kmers in the provided arrayref of sequences (Bio::Seq
                     or Bio::SeqFeature objects)
           -ids      if specified, index the sequences provided to -seq using the
                     the IDs in this arrayref instead of using the sequences
                     $seq->id() method
           -file     count kmers in the provided file of sequences
           -weights  if specified, assign the abundance of each sequence from the
                     values in this arrayref
 Returns : Grinder::KmerCollection object

k

 Usage   : $col->k;
 Function: Get the length of the kmers
 Args    : None
 Returns : Positive integer

weights

 Usage   : $col->weights({'seq1' => 3, 'seq10' => 0.45});
 Function: Get or set the weight of each sequence. Each sequence is given a
           weight of 1 by default.
 Args    : hashref where the keys are sequence IDs and the values are the weight
           of the corresponding (e.g. their relative abundance)
 Returns : Grinder::KmerCollection object

collection_by_kmer

 Usage   : $col->collection_by_kmer;
 Function: Get the collection of kmers, indexed by kmer
 Args    : None
 Returns : A hashref of hashref of arrayref:
              hash->{kmer}->{ID of sequences with this kmer}->[starts of kmer on sequence]

collection_by_seq

 Usage   : $col->collection_by_seq;
 Function: Get the collection of kmers, indexed by sequence ID
 Args    : None
 Returns : A hashref of hashref of arrayref:
              hash->{ID of sequences with this kmer}->{kmer}->[starts of kmer on sequence]

add_file

 Usage   : $col->add_file('seqs.fa');
 Function: Process the kmers in the given file of sequences.
 Args    : filename
 Returns : Grinder::KmerCollection object

add_seqs

 Usage   : $col->add_seqs([$seq1, $seq2]);
 Function: Process the kmers in the given sequences.
 Args    : * arrayref of Bio::Seq or Bio::SeqFeature objects
           * arrayref of IDs to use for the indexing of the sequences
 Returns : Grinder::KmerCollection object

filter_rare

 Usage   : $col->filter_rare( 2 );
 Function: Remove kmers occurring at less than the (weighted) abundance specified
 Args    : integer
 Returns : Grinder::KmerCollection object

filter_shared

 Usage   : $col->filter_shared( 2 );
 Function: Remove kmers occurring in less than the number of sequences specified
 Args    : integer
 Returns : Grinder::KmerCollection object

counts

 Usage   : $col->counts
 Function: Calculate the total count of each kmer. Counts are affected by the
           weights given to the sequences.
 Args    : * restrict sequences to search to specified sequence ID (optional)
           * starting position from which counting should start (optional)
           * 0 to report counts (default), 1 to report frequencies (normalize to 1)
 Returns : * arrayref of the different kmers
           * arrayref of the corresponding total counts

sources

 Usage   : $col->sources()
 Function: Return the sources of a kmer and their (weighted) abundance.
 Args    : * kmer to get the sources of
           * sources to exclude from the results (optional)
           * 0 to report counts (default), 1 to report frequencies (normalize to 1)
 Returns : * arrayref of the different sources
           * arrayref of the corresponding total counts
           If the kmer requested does not exist, the array will be empty.

kmers

 Usage   : $col->kmers('seq1');
 Function: This is the inverse of sources(). Return the kmers found in a sequence
           (given its ID) and their (weighted) abundance.
 Args    : * sequence ID to get the kmers of
           * 0 to report counts (default), 1 to report frequencies (normalize to 1)
 Returns : * arrayref of sequence IDs
           * arrayref of the corresponding total counts
           If the sequence ID requested does not exist, the arrays will be empty.

positions

 Usage   : $col->positions()
 Function: Return the positions of the given kmer on a given sequence. An error
           is reported if the kmer requested does not exist
 Args    : * desired kmer
           * desired sequence with this kmer
 Returns : Arrayref of the different positions. The arrays will be empty if the
           desired combination of kmer and sequence was not found.

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