Bioperl: amend Bio::Tools::SeqWords.pm (Comments please)

Gatherer, D. (Derek) D.Gatherer@organon.nhe.akzonobel.nl
Fri, 28 Apr 2000 12:33:26 +0200


>From Derek:  Please comment.  I hope the module will be more generally
usable in the proposed amended form below. 

...................................
For the next branch, I'm proposing to amend Bio::Tools::SeqWords.pm.  It now
counts overlapping words as well as non-overlapping ones.  The methods are
renamed: the old count_words() becomes count_non_overlap_words(), and there
is a new count_overlap_words()

The code and POD are below.  Please excuse my interpolated debugging lines.
They'll be removed from the final version.

#---------------------------------------------------------------------------
--
# PACKAGE    : SeqWords.pm
# PURPOSE    : To count n-mers in any sequence of characters
# AUTHOR     : Derek Gatherer (D.Gatherer@organon.nhe.akzonobel.nl)
# SOURCE     : 
# CREATED    : 21st March 2000
# MODIFIED   : 30th March 2000 (one bug removed, POD revised)
#	       : 24th April 2000 (POD typos corrected)
#	       : 25th April 2000: rewrite to allow for overlapping etc.
# DISCLAIMER : I am employed in the pharmaceutical industry but my 
#	       : employers do not endorse or sponsor this module
#	       : in any way whatsoever.  The above email address is
#	       : given purely for the purpose of easy communication
#            : with the author, and does not imply any connection
#	       : between my employers and anything written below.
# LICENCE    : You may distribute this module under the same terms 
#	       : as the rest of BioPerl.
#---------------------------------------------------------------------------
--

=head1 NAME

Bio::Tools::SeqWords - Object holding n-mer statistics for one sequence

=head1 SYNOPSIS

Take a sequence object from eg, an inputstream, and creates an object 
for the purposes of holding n-mer word statistics about that sequence.
The sequence can be nucleic acid or protein, but the module is probably
most relevant for DNA.  The words are counted in a non-overlapping manner,
ie. in the style of a codon table, but with any word length.
For overlapping word counts, a sequence can be 'shifted' to remove the first
character and then the count repeated.  For counts on opposite strand
(DNA/RNA),
a reverse complement method should be performed, and then the count
repeated.

Creating the SeqWords object, eg:

	my $inputstream = Bio::SeqIO->new( -file => "seqfile", -format =>
'Fasta');
	my $seqobj = $inputstream->next_seq();
	my $word_obj = Bio::Tools::SeqWords->new($seqobj);

or:
	my $seqobj = Bio::PrimarySeq->new(-seq=>'[cut and paste a sequence
here]', -moltype = 'dna', -id = 'test');
	my $word_obj  =  Bio::Tools::SeqWords->new($seqobj);

obtain a hash of word counts; this can be overlapping or non-overlapping
eg:

	my $hash_ref = $word_obj->count_overlap_words($word_length);
	my $hash_ref = $word_obj->count_non_overlap_words($word_length);

display hash table, eg:

	my %hash = %$hash_ref;
	foreach my $key(sort keys %hash)
	{
		print "\n$key\t$hash{$key}";
	}

=head1 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 potential, or the calculation of periodicity
in repetitive DNA.  Triplet frequency is already handled by
Bio::Tools::SeqStats.pm (author: Peter Schattner).  There are a few possible
applications for protein, eg: 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, eg
Stanfel 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.


=head1 DEVELOPERS' NOTES

=head1 FEEDBACK

=head2 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.

  vsns-bcd-perl@lists.uni-bielefeld.de          - General discussion
  vsns-bcd-perl-guts@lists.uni-bielefeld.de     - Technically-oriented
discussion
  http://bio.perl.org/MailList.html             - About the mailing lists

=head2 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 email or the web:

  bioperl-bugs@bio.perl.org
  http://bio.perl.org/bioperl-bugs/

=head1 AUTHOR

Derek Gatherer, in the loosest sense of the word 'author'.  The general
shape of
the module is lifted directly from Peter Schattner's SeqStats.pm module.  
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. 

=head1 APPENDIX

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

=cut

package Bio::Tools::SeqWords;
use vars qw(@ISA);
use strict;

# Object preamble - inherits from Bio::Root::Object
# this code was originally written by Peter Schattner for
Bio::Tools::SeqStats.pm
# with modifications by SAC.

@ISA = qw(Bio::Root::Object);

# new() is inherited from Bio::Root::Object

# _initialize is is called from within new()

sub _initialize 
{
    	my($self,@args) = @_;
    	$self->SUPER::_initialize;

	my $seqobj = shift (@args);
    	unless  ($seqobj->isa("Bio::PrimarySeqI")) 
	{
		die("die in _init, SeqWords works only on PrimarySeqI
objects\n");
    	}
	
    	$self->{'_seqref'} = $seqobj;
   
    	return $self;
}

=head2 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.

=cut

sub count_overlap_words
{
	my $frame = 0;
	my $seqlen = 0;
	my ($self,$word_length) = @_;

	if($word_length eq "" || $word_length =~ /[a-z]/i)
	{
		die("SeqWords cannot accept non-numeric characters or a null
value in the \$word_length variable\n");
	}
	elsif ($word_length <1 || ($word_length - int($word_length)) >0)
	{
		die("SeqWords requires the word length to be a positive
integer\n");
    	}
	
	my $seqobj =  $self->{'_seqref'};

	unless  ($seqobj->isa("Bio::PrimarySeqI")) 
	{
		die("die in count words, SeqWords works only on PrimarySeqI
objects\n");
    	}

	my $seqstring = uc $seqobj->seq();
	if(length($seqstring)>0 && $word_length > length($seqstring))
	{
		die("die in count words, \$word_length is bigger than
sequence length\n");
	}
	
	my %codon = ();

# now the real business
	
	$seqlen = $seqobj->length();			# measure length
	for ($frame = 1; $frame<=$word_length; $frame++)# run through frames
	{
		#print "\nwe are in frame $frame";	
		my $seqstring = uc($seqobj->subseq($frame,$seqlen));# take
the relevant substring
		#print "\nwhich means ... ",$seqobj->display_id,", start of
seq ", substr($seqstring,1,10),"\n";

		while($seqstring =~ /(([A-Z]){$word_length})/gim)
		{
			$codon{uc($1)}++;		# keep adding to
hash
		}
	}
	return \%codon;

# and that's that one
}

=head2 count_non_overlap_words

 Title   : count_non_overlap_words
 Usage   : $word_count = $word_obj->count_non_overlap_words($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

  Throws an exception word length is not a positive integer
  or if word length is longer than the sequence.

=cut

sub count_non_overlap_words
{
	my ($self,$word_length) = @_;

	if($word_length eq "" || $word_length =~ /[a-z]/i)
	{
		die("SeqWords cannot accept non-numeric characters or a null
value in the \$word_length variable\n");
	}
	elsif ($word_length <1 || ($word_length - int($word_length)) >0)
	{
		die("SeqWords requires the word length to be a positive
integer\n");
    	}
	
	my $seqobj =  $self->{'_seqref'};

	unless  ($seqobj->isa("Bio::PrimarySeqI")) 
	{
		die("die in count words, SeqWords works only on PrimarySeqI
objects\n");
    	}

	my $seqstring = uc $seqobj->seq();
	if($word_length > length($seqstring))
	{
		#die("die in count words, \$word_length is bigger than
sequence length\n");
		print "\nfunny business at ";
		my $name = $seqobj->display_id();
		print "\nlength is supposed only to be ";
		print length($seqstring);
		print $name;
	}
	
	my %codon = ();

# now the real business

	while($seqstring =~ /(([A-Z]){$word_length})/gim)
	{
		$codon{uc($1)}++;
	}
	return \%codon;

# and that's it
}
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