NAME¶
Bio::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);
DESCRIPTION¶
Bio::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:
https://redmine.open-bio.org/projects/bioperl/
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.