comparison variant_effect_predictor/Bio/SeqUtils.pm @ 0:2bc9b66ada89 draft default tip

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# $Id: SeqUtils.pm,v 1.11.2.1 2003/08/11 20:11:17 jason Exp $
#
# BioPerl module for Bio::SeqUtils
#
# Cared for by Heikki Lehvaslaiho <[e-mail]>
#
# Copyright Heikki Lehvaslaiho
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

Bio::SeqUtils - Additional methods for PrimarySeq objects

=head1 SYNOPSIS

    use Bio::SeqUtils;
    # get a Bio::PrimarySeqI compliant object, $seq, somehow
    $util = new Bio::SeqUtils;
    $polypeptide_3char = $util->seq3($seq);
    # or
    $polypeptide_3char = Bio::SeqUtils->seq3($seq);

    # set the sequence string (stored in one char code in the object)
    Bio::SeqUtils->seq3($seq, $polypeptide_3char);

    # translate a sequence in all six frames
    @seqs = Bio::SeqUtils->translate_6frames($seq);

=head1 DESCRIPTION

This class is a holder of methods that work on Bio::PrimarySeqI-
compliant sequence objects, e.g. Bio::PrimarySeq and
Bio::Seq. These methods are not part of the Bio::PrimarySeqI
interface and should in general not be essential to the primary function
of sequence objects. If you are thinking of adding essential
functions, it might be better to create your own sequence class.
See L<Bio::PrimarySeqI>, L<Bio::PrimarySeq>, and L<Bio::Seq> for more.

The methods take as their first argument a sequence object. It is
possible to use methods without first creating a SeqUtils object,
i.e. use it as an anonymous hash.

The first two methods, seq3() and seq3in(), give out or read in protein
sequences coded in three letter IUPAC amino acid codes.

The next two methods, translate_3frames() and translate_6frames(), wrap
around the standard translate method to give back an array of three
forward or all six frame translations.

=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.

  [e-mail]          - General 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:

  [e-mail]
  http://bugzilla.bioperl.org/

=head1 AUTHOR - Heikki Lehvaslaiho

Email:  [e-mail]
Address:

     EMBL Outstation, European Bioinformatics Institute
     Wellcome Trust Genome Campus, Hinxton
     Cambs. CB10 1SD, United Kingdom

=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::SeqUtils;
use vars qw(@ISA %ONECODE %THREECODE);
use strict;
use Carp;

@ISA = qw(Bio::Root::Root);
# new inherited from RootI

BEGIN {

    %ONECODE =
    ('Ala' => 'A', 'Asx' => 'B', 'Cys' => 'C', 'Asp' => 'D',
     'Glu' => 'E', 'Phe' => 'F', 'Gly' => 'G', 'His' => 'H',
     'Ile' => 'I', 'Lys' => 'K', 'Leu' => 'L', 'Met' => 'M',
     'Asn' => 'N', 'Pro' => 'P', 'Gln' => 'Q', 'Arg' => 'R',
     'Ser' => 'S', 'Thr' => 'T', 'Val' => 'V', 'Trp' => 'W',
     'Xaa' => 'X', 'Tyr' => 'Y', 'Glx' => 'Z', 'Ter' => '*',
     'Sec' => 'U'
     );

    %THREECODE =
    ('A' => 'Ala', 'B' => 'Asx', 'C' => 'Cys', 'D' => 'Asp',
     'E' => 'Glu', 'F' => 'Phe', 'G' => 'Gly', 'H' => 'His',
     'I' => 'Ile', 'K' => 'Lys', 'L' => 'Leu', 'M' => 'Met',
     'N' => 'Asn', 'P' => 'Pro', 'Q' => 'Gln', 'R' => 'Arg',
     'S' => 'Ser', 'T' => 'Thr', 'V' => 'Val', 'W' => 'Trp',
     'Y' => 'Tyr', 'Z' => 'Glx', 'X' => 'Xaa', '*' => 'Ter',
     'U' => 'Sec'
     );
}

=head2 seq3

 Title   : seq3
 Usage   : $string = Bio::SeqUtils->seq3($seq)
 Function:

           Read only method that returns the amino acid sequence as a
           string of three letter codes. alphabet has to be
           'protein'. Output follows the IUPAC standard plus 'Ter' for
           terminator. Any unknown character, including the default
           unknown character 'X', is changed into 'Xaa'. A noncoded
           aminoacid selenocystein is recognized (Sec, U).

 Returns : A scalar
 Args    : character used for stop in the protein sequence optional,
           defaults to '*' string used to separate the output amino
           acid codes, optional, defaults to ''

=cut

sub seq3 {
   my ($self, $seq, $stop, $sep ) = @_;

   $seq->isa('Bio::PrimarySeqI') ||
       $self->throw('Not a Bio::PrimarySeqI object but [$self]');
   $seq->alphabet eq 'protein' ||
       $self->throw('Not a protein sequence');

   if (defined $stop) {
       length $stop != 1 and $self->throw('One character stop needed, not [$stop]');
       $THREECODE{$stop} = "Ter";
   }
   $sep ||= '';

   my $aa3s;
   foreach my $aa  (split //, uc $seq->seq) {
       $THREECODE{$aa} and $aa3s .= $THREECODE{$aa}. $sep, next;
       $aa3s .= 'Xaa'. $sep;
   }
   $sep and substr($aa3s, -(length $sep), length $sep) = '' ;
   return $aa3s;
}

=head2 seq3in

 Title   : seq3in
 Usage   : $string = Bio::SeqUtils->seq3in($seq, 'MetGlyTer')
 Function:

           Method for in-place changing of the sequence of a
           Bio::PrimarySeqI sequence object. The three letter amino
           acid input string is converted into one letter code.  Any
           unknown character triplet, including the default 'Xaa', is
           converted into 'X'.

 Returns : Bio::PrimarySeq object;
 Args    : character to be used for stop in the protein seqence,
              optional, defaults to '*'
           character to be used for unknown in the protein seqence,
              optional, defaults to 'X'

=cut

sub seq3in {
   my ($self, $seq, $string, $stop, $unknown) = @_;

   $seq->isa('Bio::PrimarySeqI') ||
       $self->throw('Not a Bio::PrimarySeqI object but [$self]');
   $seq->alphabet eq 'protein' ||
       $self->throw('Not a protein sequence');

   if (defined $stop) {
       length $stop != 1 and $self->throw('One character stop needed, not [$stop]');
       $ONECODE{'Ter'} = $stop;
   }
   if (defined $unknown) {
       length $unknown != 1 and $self->throw('One character stop needed, not [$unknown]');
       $ONECODE{'Xaa'} = $unknown;
   }

   my ($aas, $aa3);
   my $length = (length $string) - 2;
   for (my $i = 0 ; $i < $length ; $i += 3)  {
       $aa3 = substr($string, $i, 3);
       $ONECODE{$aa3} and $aas .= $ONECODE{$aa3}, next;
       $aas .= 'X';
   }
   $seq->seq($aas);
   return $seq;
}

=head2 translate_3frames

 Title   : translate_3frames
 Usage   : @prots = Bio::SeqUtils->translate_3frames($seq)
 Function: Translate a nucleotide sequence in three forward frames.
           The IDs of the sequences are appended with '-0F', '-1F', '-2F'.
 Returns : An array of seq objects
 Args    : sequence object
           same arguments as to Bio::PrimarySeqI::translate

=cut

sub translate_3frames {
    my ($self, $seq, @args ) = @_;
    
    $self->throw('Object [$seq] '. 'of class ['. ref($seq).  ']  can not be translated.')
	unless $seq->can('translate');

    my ($stop, $unknown, $frame, $tableid, $fullCDS, $throw) = @args;
    my @seqs;
    my $f = 0;
    while ($f != 3) {
        my $translation = $seq->translate($stop, $unknown,$f,$tableid, $fullCDS, $throw );
	$translation->id($seq->id. "-". $f. "F");
	push @seqs, $translation;
	$f++;
    }

    return @seqs;
}

=head2 translate_6frames

 Title   : translate_6frames
 Usage   : @prots = Bio::SeqUtils->translate_6frames($seq)
 Function: translate a nucleotide sequence in all six frames
           The IDs of the sequences are appended with '-0F', '-1F', '-2F',
           '-0R', '-1R', '-2R'.
 Returns : An array of seq objects
 Args    : sequence object
           same arguments as to Bio::PrimarySeqI::translate

=cut

sub translate_6frames {
    my ($self, $seq, @args ) = @_;
    
    my @seqs = $self->translate_3frames($seq, @args);
    $seq->seq($seq->revcom->seq);
    my @seqs2 = $self->translate_3frames($seq, @args);
    foreach my $seq2 (@seqs2) {
	my ($tmp) = $seq2->id;
	$tmp =~ s/F$/R/g;
	$seq2->id($tmp);
    }
    return @seqs, @seqs2;
}


=head2 valid_aa

 Title   : valid_aa
 Usage   : my @aa = $table->valid_aa
 Function: Retrieves a list of the valid amino acid codes.
           The list is ordered so that first 21 codes are for unique 
           amino acids. The rest are ['B', 'Z', 'X', '*'].
 Returns : array of all the valid amino acid codes
 Args    : [optional] $code => [0 -> return list of 1 letter aa codes,
				1 -> return list of 3 letter aa codes,
				2 -> return associative array of both ]

=cut

sub valid_aa{
   my ($self,$code) = @_;

   if( ! $code ) { 
       my @codes;
       foreach my $c ( sort values %ONECODE ) {
	   push @codes, $c unless ( $c =~ /[BZX\*]/ );
       }
       push @codes, qw(B Z X *); # so they are in correct order ?
       return @codes;
  }
   elsif( $code == 1 ) { 
       my @codes;
       foreach my $c ( sort keys %ONECODE ) {
	   push @codes, $c unless ( $c =~ /(Asx|Glx|Xaa|Ter)/ );
       }
       push @codes, ('Asx', 'Glx', 'Xaa', 'Ter' );
       return @codes;
   }
   elsif( $code == 2 ) { 
       my %codes = %ONECODE;
       foreach my $c ( keys %ONECODE ) {
	   my $aa = $ONECODE{$c};
	   $codes{$aa} = $c;
       }
       return %codes;
   } else {
       $self->warn("unrecognized code in ".ref($self)." method valid_aa()");
       return ();
   }
}

1;