Bio::Tools::SeqWords(3User Contributed Perl DocumentatiBio::Tools::SeqWords(3)NAMEBio::Tools::SeqWords - Object holding n-mer statistics for a sequence
SYNOPSIS
# Create the SeqWords object, e.g.:
my $inputstream = Bio::SeqIO->new(-file => "seqfile",
-format => 'Fasta');
my $seqobj = $inputstream->next_seq();
my $seq_word = Bio::Tools::SeqWords->new(-seq => $seqobj);
# Or:
my $seqobj = Bio::PrimarySeq->new(-seq => "agggtttccc",
-alphabet => 'dna',
-id => 'test');
my $seq_word = Bio::Tools::SeqWords->new(-seq => $seqobj);
# obtain a hash of word counts, eg:
my $hash_ref = $seq_stats->count_words($word_length);
# display hash table, eg:
my %hash = %$hash_ref;
foreach my $key(sort keys %hash)
{
print "\n$key\t$hash{$key}";
}
# Or:
my $hash_ref =
Bio::Tools::SeqWords->count_words($seqobj,$word_length);
DESCRIPTIONBio::Tools::SeqWords is a featherweight object for the calculation of
n-mer word occurrences in a single sequence. It is envisaged that the
object will be useful for construction of scripts which use n-mer word
tables as the raw material for statistical calculations; for instance,
hexamer frequency for the calculation of coding protential, or the
calculation of periodicity in repetitive DNA. Triplet frequency is
already handled by Bio::Tools::SeqStats (author: Peter Schattner).
There are a few possible applications for protein, e.g. hypothesised
amino acid 7-mers in heat shock proteins, or proteins with multiple
simple motifs. Sometimes these protein periodicities are best seen
when the amino acid alphabet is truncated, e.g. Shulman alphabet.
Since there are quite a few of these shortened alphabets, this module
does not specify any particular alphabet.
See Synopsis above for object creation code.
Rationale
Take a sequence object and create an object for the purposes of holding
n-mer word statistics about that sequence. The sequence can be nucleic
acid or protein.
In count_words() the words are counted in a non-overlapping manner, ie.
in the style of a codon table, but with any word length.
In count_overlap_words() the words are counted in an overlapping
manner.
For counts on opposite strand (DNA/RNA), a reverse complement method
should be performed, and then the count repeated.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and
data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
http://bugzilla.open-bio.org/
AUTHOR
Derek Gatherer, in the loosest sense of the word 'author'. The general
shape of the module is lifted directly from the SeqStat module of Peter
Schattner. The central subroutine to count the words is adapted from
original code provided by Dave Shivak, in response to a query on the
bioperl mailing list. At least 2 other people provided alternative
means (equally good but not used in the end) of performing the same
calculation. Thanks to all for your assistance.
CONTRIBUTORS
Jason Stajich, jason-at-bioperl.org
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
count_words
Title : count_words
Usage : $word_count = $seq_stats->count_words($word_length)
or
$word_count = $seq_stats->Bio::Tools::SeqWords->($seqobj,$word_length);
Function: Counts non-overlapping words within a string, any alphabet is
used
Example : a sequence ACCGTCCGT, counted at word length 4, will give the hash
{ACCG => 1, TCCG => 1}
Returns : Reference to a hash in which keys are words (any length) of the
alphabet used and values are number of occurrences of the word
in the sequence.
Args : Word length as scalar and, reference to sequence object if
required
Throws an exception word length is not a positive integer
or if word length is longer than the sequence.
count_overlap_words
Title : count_overlap_words
Usage : $word_count = $word_obj->count_overlap_words($word_length);
Function: Counts overlapping words within a string, any alphabet is used
Example : A sequence ACCAACCA, counted at word length 4, will give the hash
{ACCA=>2, CCAA=>1, CAAC=>1, AACC=>1}
Returns : Reference to a hash in which keys are words (any length) of the
alphabet used and values are number of occurrences of the word in
the sequence.
Args : Word length as scalar
Throws an exception if word length is not a positive integer
or if word length is longer than the sequence.
perl v5.14.1 2011-07-22 Bio::Tools::SeqWords(3)
