Raw content of Bio::SeqUtils # $Id: SeqUtils.pm,v 2003/08/11 20:11:17 jason Exp $ # # BioPerl module for Bio::SeqUtils # # Cared for by Heikki Lehvaslaiho <heikki@ebi.ac.uk> # # 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. bioperl-l@bioperl.org - 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: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Heikki Lehvaslaiho Email: heikki@ebi.ac.uk 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;