libbio-perl-perl 1.6.901-3 / usr / share / perl5 / Bio / Tools / IUPAC.pm

#
# BioPerl module for IUPAC
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Aaron Mackey <amackey@virginia.edu>
#
# Copyright Aaron Mackey
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

Bio::Tools::IUPAC - Generates unique Seq objects from an ambiguous Seq object

=head1 SYNOPSIS

 use Bio::Seq;
 use Bio::Tools::IUPAC;

 my $ambiseq = Bio::Seq->new(-seq => 'ARTCGUTGR', -alphabet => 'dna');
 my $stream  = Bio::Tools::IUPAC->new(-seq => $ambiseq);

 while ($uniqueseq = $stream->next_seq()) {
     # process the unique Seq object.
 }

=head1 DESCRIPTION

IUPAC is a tool that produces a stream of unique, "strict"-satisfying Seq
objects from an ambiquous Seq object (containing non-standard characters given
the meaning shown below)

        Extended DNA / RNA alphabet :
        (includes symbols for nucleotide ambiguity)
        ------------------------------------------
        Symbol       Meaning      Nucleic Acid
        ------------------------------------------
         A            A           Adenine
         C            C           Cytosine
         G            G           Guanine
         T            T           Thymine
         U            U           Uracil
         M          A or C
         R          A or G
         W          A or T
         S          C or G
         Y          C or T
         K          G or T
         V        A or C or G
         H        A or C or T
         D        A or G or T
         B        C or G or T
         X      G or A or T or C
         N      G or A or T or C

        IUPAC-IUB SYMBOLS FOR NUCLEOTIDE NOMENCLATURE:
          Cornish-Bowden (1985) Nucl. Acids Res. 13: 3021-3030.

-----------------------------------

       Amino Acid alphabet:
        ------------------------------------------
        Symbol           Meaning
        ------------------------------------------
        A        Alanine
        B        Aspartic Acid, Asparagine
        C        Cystine
        D        Aspartic Acid
        E        Glutamic Acid
        F        Phenylalanine
        G        Glycine
        H        Histidine
        I        Isoleucine
        J        Isoleucine/Leucine
        K        Lysine
        L        Leucine
        M        Methionine
        N        Asparagine
        O        Pyrrolysine
        P        Proline
        Q        Glutamine
        R        Arginine
        S        Serine
        T        Threonine
        U        Selenocysteine
        V        Valine
        W        Tryptophan
        X        Unknown
        Y        Tyrosine
        Z        Glutamic Acid, Glutamine
        *        Terminator


        IUPAC-IUP AMINO ACID SYMBOLS:
          Biochem J. 1984 Apr 15; 219(2): 345-373
          Eur J Biochem. 1993 Apr 1; 213(1): 2

=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.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Support 

Please direct usage questions or support issues to the mailing list:

I<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.

=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 the
web:

  https://redmine.open-bio.org/projects/bioperl/

=head1 AUTHOR - Aaron Mackey

Email amackey-at-virginia.edu

=head1 APPENDIX

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

=cut


# Let the code begin...

package Bio::Tools::IUPAC;

use strict;
use vars qw(%IUP %IUB %REV_IUB $AUTOLOAD);

BEGIN {
    %IUB = ( A => [qw(A)],
	     C => [qw(C)],
	     G => [qw(G)],
	     T => [qw(T)],
	     U => [qw(U)],
	     M => [qw(A C)],
	     R => [qw(A G)],
	     W => [qw(A T)],
	     S => [qw(C G)],
	     Y => [qw(C T)],
	     K => [qw(G T)],
	     V => [qw(A C G)],
	     H => [qw(A C T)],
	     D => [qw(A G T)],
	     B => [qw(C G T)],
	     X => [qw(G A T C)],
	     N => [qw(G A T C)]
	     );
	%REV_IUB = (A	=> 'A',
				T	=> 'T',
				C	=> 'C',
				G 	=> 'G',
				AC	=> 'M',
				AG	=> 'R',
				AT	=> 'W',
				CG	=> 'S',
				CT	=> 'Y',
				'GT'	=> 'K',
				ACG	=> 'V',
				ACT	=> 'H',
				AGT	=> 'D',
				CGT	=> 'B',
				ACGT=> 'N',
				N	=> 'N'
				);


    %IUP = (A => [qw(A)],
	    B => [qw(D N)],
	    C => [qw(C)],
	    D => [qw(D)],
	    E => [qw(E)],
	    F => [qw(F)],
	    G => [qw(G)],
	    H => [qw(H)],
	    I => [qw(I)],
        J => [qw(I L)],
	    K => [qw(K)],
	    L => [qw(L)],
	    M => [qw(M)],
	    N => [qw(N)],
        O => [qw(O)],
	    P => [qw(P)],
	    Q => [qw(Q)],
	    R => [qw(R)],
	    S => [qw(S)],
	    T => [qw(T)],
	    U => [qw(U)],
	    V => [qw(V)],
	    W => [qw(W)],
	    X => [qw(X)],
	    Y => [qw(Y)],
	    Z => [qw(E Q)],
	    '*' => ['*']
	    );

}
use base qw(Bio::Root::Root);

=head2 new

 Title   : new
 Usage   : Bio::Tools::IUPAC->new( $seq)
 Function: returns a new seq stream (akin to SeqIO)
 Returns : a Bio::Tools::IUPAC stream object that will produce unique
           Seq objects on demand.
 Args    : an ambiguously coded Seq.pm object that has a specified 'alphabet'


=cut


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

    my ($seq) = $self->_rearrange([qw(SEQ)],@args);
    if((! defined($seq)) && @args && ref($args[0])) {
	# parameter not passed as named parameter?
	$seq = $args[0];
    }
    $seq->isa('Bio::Seq') or
	$self->throw("Must supply a Seq.pm object to IUPAC!");
    $self->{'_SeqObj'} = $seq;
    if ($self->{'_SeqObj'}->alphabet() =~ m/^[dr]na$/i ) {
        # nucleotide seq object
	$self->{'_alpha'} = [ map { $IUB{uc($_)} }
			      split('', $self->{'_SeqObj'}->seq()) ];
    } elsif ($self->{'_SeqObj'}->alphabet() =~ m/^protein$/i ) {
        # amino acid seq object
	$self->{'_alpha'} = [ map { $IUP{uc($_)} }
			       split('', $self->{'_SeqObj'}->seq()) ];
    } else { # unknown type: we could make a guess, but let's not.
	$self->throw("You must specify the 'type' of sequence provided to IUPAC");
    }
    $self->{'_string'} = [(0) x length($self->{'_SeqObj'}->seq())];
    scalar @{$self->{'_string'}} or $self->throw("Sequence has zero-length!");
    $self->{'_string'}->[0] = -1;
    return $self;
}

=head2 next_seq

 Title   : next_seq
 Usage   : $iupac->next_seq()
 Function: returns the next unique Seq object
 Returns : a Seq.pm object
 Args    : none.


=cut

sub next_seq{
    my ($self) = @_;

    for my $i ( 0 .. $#{$self->{'_string'}} ) {
	next unless $self->{'_string'}->[$i] || @{$self->{'_alpha'}->[$i]} > 1;
	if ( $self->{'_string'}->[$i] == $#{$self->{'_alpha'}->[$i]} ) { # rollover
	    if ( $i == $#{$self->{'_string'}} ) { # end of possibilities
		return;
	    } else {
		$self->{'_string'}->[$i] = 0;
		next;
	    }
	} else {
	    $self->{'_string'}->[$i]++;
	    my $j = -1;
	    $self->{'_SeqObj'}->seq(join('', map { $j++; $self->{'_alpha'}->[$j]->[$_]; } @{$self->{'_string'}}));
	    my $desc = $self->{'_SeqObj'}->desc();
	    if ( !defined $desc ) { $desc = ""; }

	    $self->{'_num'}++;
	    1 while $self->{'_num'} =~ s/(\d)(\d\d\d)(?!\d)/$1,$2/;
	    $desc =~ s/( \[Bio::Tools::IUPAC-generated\sunique sequence # [^\]]*\])|$/ \[Bio::Tools::IUPAC-generated unique sequence # $self->{'_num'}\]/;
	    $self->{'_SeqObj'}->desc($desc);
	    $self->{'_num'} =~ s/,//g;
	    return $self->{'_SeqObj'};
	}
    }
}

=head2 iupac_iup

 Title   : iupac_iup
 Usage   : my %aasymbols = $iupac->iupac_iup
 Function: Returns a hash of PROTEIN symbols -> symbol components
 Returns : Hash
 Args    : none

=cut

sub iupac_iup{
   return %IUP;

}

=head2 iupac_iub

 Title   : iupac_iub
 Usage   : my %dnasymbols = $iupac->iupac_iub
 Function: Returns a hash of DNA symbols -> symbol components
 Returns : Hash
 Args    : none

=cut

sub iupac_iub{
   return %IUB;
}

=head2 iupac_rev_iub

 Title   : iupac_rev_iub
 Usage   : my %dnasymbols = $iupac->iupac_rev_iub
 Function: Returns a hash of nucleotide combinations -> IUPAC code
           (a reverse of the iupac_iub hash).
 Returns : Hash
 Args    : none

=cut

sub iupac_rev_iub{
   return %REV_IUB;
}

=head2 count

 Title   : count
 Usage   : my $total = $iupac->count();
 Function: Calculates the number of unique, unambiguous sequences that
           this ambiguous sequence could generate
 Return  : int
 Args    : none

=cut

sub count {
    my ($self) = @_;

    my $count = 1;
    $count *= scalar(@$_) for (@{$self->{'_alpha'}});
    return $count;
}


sub AUTOLOAD {

    my $self = shift @_;
    my $method = $AUTOLOAD;
    $method =~ s/.*:://;
    return $self->{'_SeqObj'}->$method(@_)
	unless $method eq 'DESTROY';
}

1;