Bio::Tools OddCodes
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Summary
Bio::Tools::OddCodes - Object holding alternative alphabet coding for
one protein sequence
Package variables
No package variables defined.
Included modules
Bio::Root::Root
Inherit
Bio::Root::Root
Synopsis
Take a sequence object from eg, an inputstream, and creates an object
for the purposes of rewriting that sequence in another alphabet.
These are abbreviated amino acid sequence alphabets, designed to
simplify the statistical aspects of analysing protein sequences, by
reducing the combinatorial explosion of the 20-letter alphabet. These
abbreviated alphabets range in size from 2 to 8.
Creating the OddCodes object, eg:
	my $inputstream = Bio::SeqIO->new( '-file' => "seqfile", 
                                           '-format' => 'Fasta');
	my $seqobj = $inputstream->next_seq();
	my $oddcode_obj = Bio::Tools::Oddcodes->new(-seq => $seqobj);
or:
	my $seqobj = Bio::PrimarySeq->new
              (-seq=>'[cut and paste a sequence here]',
               -alphabet => 'protein',
               -id => 'test');
	my $oddcode_obj  =  Bio::Tools::OddCodes->new(-seq => $seqobj);
do the alternative coding, returning the answer as a reference to a string
	my $output = $oddcode_obj->structural();
	my $output = $oddcode_obj->chemical();
	my $output = $oddcode_obj->functional();
	my $output = $oddcode_obj->charge();
	my $output = $oddcode_obj->hydrophobic();
	my $output = $oddcode_obj->Dayhoff();
	my $output = $oddcode_obj->Sneath();
	my $output = $oddcode_obj->Stanfel();
display sequence in new form, eg:
	my $new_coding = $$output;
	print "\n$new_coding";
Description
Bio::Tools::Oddcodes is a welterweight object for rewriting a protein
sequence in an alternative alphabet. 8 of these are provided, ranging
from the the 2-letter hydrophobic alphabet, to the 8-letter chemical
alphabet. These are useful for the statistical analysis of protein
sequences since they can partially avoid the combinatorial explosion
produced by the full 20-letter alphabet (eg. 400 dimers, 8000 trimers
etc.)
The objects will print out a warning if the input sequence is not a
protein. If you know what you are doing, you can silence the warning
by setting verbose() to a negetive value.
See Synopsis above for object creation code.
Methods
Dayhoff()
No description
Code
Sneath()
No description
Code
Stanfel()
No description
Code
_pullseq
No description
Code
charge()
No description
Code
chemical()
No description
Code
functional()
No description
Code
hydrophobic()
No description
Code
new
No description
Code
structural()
No description
Code
Methods description
None available.
Methods code
Dayhoff()descriptionprevnextTop
sub Dayhoff() {
	my $self = $_[0];
	my $seqstring = &_pullseq($self);

# now the real business
	
	$seqstring =~ tr/[C]/1/;
	$seqstring =~ tr/[AGPST]/2/;
	$seqstring =~ tr/[DENQ]/3/;
	$seqstring =~ tr/[HKR]/4/;
	$seqstring =~ tr/[ILMV]/5/;
	$seqstring =~ tr/[FWY]/6/;
	$seqstring =~ tr/1/A/;
	$seqstring =~ tr/2/C/;
	$seqstring =~ tr/3/D/;
	$seqstring =~ tr/4/E/;
	$seqstring =~ tr/5/F/;
	$seqstring =~ tr/6/G/;

	return\$ seqstring;

# and that's that one
}
Sneath()descriptionprevnextTop
sub Sneath() {
	my $self = $_[0];
	my $seqstring = &_pullseq($self);

# now the real business
	
	$seqstring =~ tr/[ILV]/1/;
	$seqstring =~ tr/[AGP]/2/;
	$seqstring =~ tr/[MNQ]/3/;
	$seqstring =~ tr/[CST]/4/;
	$seqstring =~ tr/[DE]/5/;
	$seqstring =~ tr/[KR]/6/;
	$seqstring =~ tr/[FHWY]/7/;
	$seqstring =~ tr/1/A/;
	$seqstring =~ tr/2/C/;
	$seqstring =~ tr/3/D/;
	$seqstring =~ tr/4/E/;
	$seqstring =~ tr/5/F/;
	$seqstring =~ tr/6/G/;
	$seqstring =~ tr/7/H/;

	return\$ seqstring;

# and that's that one
}
Stanfel()descriptionprevnextTop
sub Stanfel() {
	my $self = $_[0];
	my $seqstring = &_pullseq($self);

# now the real business
	
	$seqstring =~ tr/[ACGILMPSTV]/1/;
	$seqstring =~ tr/[DENQ]/2/;
	$seqstring =~ tr/[FWY]/3/;
	$seqstring =~ tr/[HKR]/4/;
	$seqstring =~ tr/1/A/;
	$seqstring =~ tr/2/C/;
	$seqstring =~ tr/3/D/;
	$seqstring =~ tr/4/E/;

	return\$ seqstring;

# and that's that one
}
_pullseqdescriptionprevnextTop
sub _pullseq {
	my $self = $_[0];

	my $seqobj =  $self->{'_seqref'};
	
	unless  ($seqobj->isa("Bio::PrimarySeqI")) 
	{
		die("die, OddCodes works only on PrimarySeqI objects\n");
    	}
        $self->warn("\tAll OddCode alphabets need a protein sequence,\n".
                    "\tbut BioPerl thinks this is not: [". $seqobj->id. "]")
            unless $seqobj->alphabet eq 'protein' or $self->verbose < 0;;

	my $seqstring = uc $seqobj->seq();

	if(length($seqstring)<1)
	{
		die("$seqstring: die, sequence has zero length\n");
	}
	return $seqstring;
}

1;
}
charge()descriptionprevnextTop
sub charge() {
	my $self = $_[0];
	my $seqstring = &_pullseq($self);

# now the real business
	
	$seqstring =~ tr/[DE]/1/;
	$seqstring =~ tr/[HKR]/2/;
	$seqstring =~ tr/[ACFGILMNPQSTVWY]/3/;
	$seqstring =~ tr/1/A/;
	$seqstring =~ tr/2/C/;
	$seqstring =~ tr/3/N/;

	return\$ seqstring;

# and that's that one
}

# _pullseq is called within each of the subroutines
# it just checks a few things and returns the sequence
}
chemical()descriptionprevnextTop
sub chemical() {
	my $self = $_[0];
	my $seqstring = &_pullseq($self);

# now the real business
	
	$seqstring =~ tr/[DE]/1/;
	$seqstring =~ tr/[AGILV]/2/;
	$seqstring =~ tr/[NQ]/3/;
	$seqstring =~ tr/[FWY]/4/;
	$seqstring =~ tr/[RHK]/5/;
	$seqstring =~ tr/[ST]/6/;
	$seqstring =~ tr/P/7/;
	$seqstring =~ tr/[CM]/8/;
	$seqstring =~ tr/1/A/;
	$seqstring =~ tr/2/L/;
	$seqstring =~ tr/3/M/;
	$seqstring =~ tr/4/R/;
	$seqstring =~ tr/5/C/;
	$seqstring =~ tr/6/H/;
	$seqstring =~ tr/7/I/;
	$seqstring =~ tr/8/S/;

	return\$ seqstring;

# and that's that one
}
functional()descriptionprevnextTop
sub functional() {
	my $self = $_[0];
	my $seqstring = &_pullseq($self);

# now the real business
	
	$seqstring =~ tr/[DE]/1/;
	$seqstring =~ tr/[HKR]/2/;
	$seqstring =~ tr/[AFILMPVW]/3/;
	$seqstring =~ tr/[CGNQSTY]/4/;
	$seqstring =~ tr/1/A/;
	$seqstring =~ tr/2/C/;
	$seqstring =~ tr/3/H/;
	$seqstring =~ tr/4/P/;

	return\$ seqstring;

# and that's that one
}
hydrophobic()descriptionprevnextTop
sub hydrophobic() {
	my $self = $_[0];
	my $seqstring = &_pullseq($self);

# now the real business
	
	$seqstring =~ tr/[AFILMPVW]/1/;
	$seqstring =~ tr/[CDEGHKNQRSTY]/2/;
	$seqstring =~ tr/1/I/;
	$seqstring =~ tr/2/O/;

	return\$ seqstring;

# and that's that one
}
newdescriptionprevnextTop
sub new {
    my($class,@args) = @_;

    my $self = $class->SUPER::new(@args);

    my ($seqobj) = $self->_rearrange([qw(SEQ)],@args);
    if((! defined($seqobj)) && @args && ref($args[0])) {
	# parameter not passed as named parameter?
	$seqobj = $args[0];
    }
    unless  ($seqobj->isa("Bio::PrimarySeqI")) 
    {
	die("die in _init, OddCodes works only on PrimarySeqI
objects\n");
    }

    $self->{'_seqref'} = $seqobj;

    return $self;
}
structural()descriptionprevnextTop
sub structural() {
	my $self = $_[0];
	my $seqstring = &_pullseq($self);	# see _pullseq() below

# now the real business
	
	$seqstring =~ tr/[ACGPSTWY]/1/;
	$seqstring =~ tr/[RNDQEHK]/2/;
	$seqstring =~ tr/[ILMFV]/3/;
	$seqstring =~ tr/1/A/;
	$seqstring =~ tr/2/E/;
	$seqstring =~ tr/3/I/;

	return\$ seqstring;

# and that's that one
}
General documentation
FEEDBACKTop
Mailing ListsTop
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://www.bioperl.org/MailList.html - About the mailing lists
Reporting BugsTop
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@bioperl.org
  http://www.bugzilla.bioperl.org/
AUTHORTop
Derek Gatherer
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
structuralTop
 Title   : structural
 Usage   : $output = $oddcode_obj->structural(); 
 Function: turns amino acid sequence into 3-letter structural alphabet
	 : A (ambivalent), E (external), I (internal)
 Example : a sequence ACDEFGH will become AAEEIAE
 Returns : Reference to the new sequence string
 Args    : none
functionalTop
 Title   : functional
 Usage   : $output = $oddcode_obj->functional(); 
 Function: turns amino acid sequence into 4-letter functional alphabet
	 : A (acidic), C (basic), H (hydrophobic), P (polar)
 Example : a sequence ACDEFGH will become HPAAHHC 
 Returns : Reference to the new sequence string
 Args    : none
hydrophobicTop
 Title   : hydrophobic
 Usage   : $output = $oddcode_obj->hydrophobic(); 
 Function: turns amino acid sequence into 2-letter hydrophobicity alphabet
	 : O (hydrophobic), I (hydrophilic)
 Example : a sequence ACDEFGH will become OIIIOII
 Returns : Reference to the new sequence string
 Args    : none
DayhoffTop
 Title   : Dayhoff
 Usage   : $output = $oddcode_obj->Dayhoff(); 
 Function: turns amino acid sequence into 6-letter Dayhoff alphabet
 Example : a sequence ACDEFGH will become CADDGCE 
 Returns : Reference to the new sequence string
 Args    : none
SneathTop
 Title   : Sneath
 Usage   : $output = $oddcode_obj->Sneath(); 
 Function: turns amino acid sequence into 7-letter Sneath alphabet
 Example : a sequence ACDEFGH will become CEFFHCF
 Returns : Reference to the new sequence string
 Args    : none
StanfelTop
 Title   : Stanfel
 Usage   : $output = $oddcode_obj->Stanfel(); 
 Function: turns amino acid sequence into 4-letter Stanfel alphabet
 Example : a sequence ACDEFGH will become AACCDAE
 Returns : Reference to the new sequence string
 Args    : none
chemical()Top
 Title   : chemical
 Usage   : $output = $oddcode_obj->chemical(); 
 Function: turns amino acid sequence into 8-letter chemical alphabet
	 : A (acidic), L (aliphatic), M (amide), R (aromatic)
	 : C (basic), H (hydroxyl), I (imino), S (sulphur)
 Example : a sequence ACDEFGH will become LSAARAC 
 Returns : Reference to the new sequence string
 Args    : none
chargeTop
 Title   : charge
 Usage   : $output = $oddcode_obj->charge(); 
 Function: turns amino acid sequence into 3-letter charge alphabet
 Example : a sequence ACDEFGH will become NNAANNC 
 Returns : Reference to the new sequence string
 Args    : none