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Bio::Tools::SeqWords(3User Contributed Perl DocumentatiBio::Tools::SeqWords(3)

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://github.com/bioperl/bioperl-live/issues

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 v5.24.1			  2017-07-08	       Bio::Tools::SeqWords(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR | CONTRIBUTORS | APPENDIX

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