Raw content of Bio::Tools::OddCodes
<![CDATA[#$Id: OddCodes.pm,v 1.10.2.1 2003/04/07 04:27:42 heikki Exp $
#-----------------------------------------------------------------------------
# PACKAGE : OddCodes.pm
# PURPOSE : To write amino acid sequences in alternative alphabets
# AUTHOR : Derek Gatherer (D.Gatherer@organon.nhe.akzonobel.nl)
# SOURCE :
# CREATED : 8th July 2000
# MODIFIED :
# 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::OddCodes - Object holding alternative alphabet coding for
one protein sequence
=head1 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$new_coding";
=head1 DESCRIPTION
Bio::Tools::Oddcodes is a welterweight object for rewriting a protein
sequence in an alternative alphabet. 8 of these are provided, ranging
from the the 2-letter hydrophobic alphabet, to the 8-letter chemical
alphabet. These are useful for the statistical analysis of protein
sequences since they can partially avoid the combinatorial explosion
produced by the full 20-letter alphabet (eg. 400 dimers, 8000 trimers
etc.)
The objects will print out a warning if the input sequence is not a
protein. If you know what you are doing, you can silence the warning
by setting verbose() to a negetive value.
See Synopsis above for object creation code.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions preferably
to one of the Bioperl mailing lists.
Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://www.bioperl.org/MailList.html - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
bioperl-bugs@bioperl.org
http://www.bugzilla.bioperl.org/
=head1 AUTHOR
Derek Gatherer
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
#'
package Bio::Tools::OddCodes;
use vars qw(@ISA);
use strict;
use Bio::Root::Root;
@ISA = qw(Bio::Root::Root);
sub new
{
my($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;
}
=head2 structural
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
=cut
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
}
=head2 functional
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
=cut
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
}
=head2 hydrophobic
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
=cut
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
}
=head2 Dayhoff
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
=cut
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
}
=head2 Sneath
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
=cut
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
}
=head2 Stanfel
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
=cut
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
}
=head2 chemical()
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
=cut
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
}
=head2 charge
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
=cut
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
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;
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