Grinder::KmerCollection(3pm) User Contributed Perl Documentation Grinder::KmerCollection(3pm)
NAME
Grinder::KmerCollection - 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 <florent.angly@gmail.com>
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
objects)
-ids if specified, index the sequences provided to -seq using the
use 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 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 you gave 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.
perl v5.14.2 2012-01-17 Grinder::KmerCollection(3pm)