Raw content of Bio::Tools::OddCodes #$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;