Raw content of Bio::PrimarySeqI # $Id: PrimarySeqI.pm,v 2003/08/29 15:37:39 birney Exp $ # # BioPerl module for Bio::PrimarySeqI # # Cared for by Ewan Birney <birney@sanger.ac.uk> # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PrimarySeqI [Developers] - Interface definition for a Bio::PrimarySeq =head1 SYNOPSIS # Bio::PrimarySeqI is the interface class for sequences. # If you are a newcomer to bioperl, you should # start with Bio::Seq documentation. This # documentation is mainly for developers using # Bioperl. # to test this is a seq object $obj->isa("Bio::PrimarySeqI") || $obj->throw("$obj does not implement the Bio::PrimarySeqI interface"); # accessors $string = $obj->seq(); $substring = $obj->subseq(12,50); $display = $obj->display_id(); # for human display $id = $obj->primary_id(); # unique id for this object, # implementation defined $unique_key= $obj->accession_number(); # unique biological id # object manipulation eval { $rev = $obj->revcom(); }; if( $@ ) { $obj->throw("Could not reverse complement. ". "Probably not DNA. Actual exception\n$@\n"); } $trunc = $obj->trunc(12,50); # $rev and $trunc are Bio::PrimarySeqI compliant objects =head1 DESCRIPTION This object defines an abstract interface to basic sequence information - for most users of the package the documentation (and methods) in this class are not useful - this is a developers only class which defines what methods have to be implmented by other Perl objects to comply to the Bio::PrimarySeqI interface. Go "perldoc Bio::Seq" or "man Bio::Seq" for more information on the main class for sequences. PrimarySeq is an object just for the sequence and its name(s), nothing more. Seq is the larger object complete with features. There is a pure perl implementation of this in Bio::PrimarySeq. If you just want to use Bio::PrimarySeq objects, then please read that module first. This module defines the interface, and is of more interest to people who want to wrap their own Perl Objects/RDBs/FileSystems etc in way that they "are" bioperl sequence objects, even though it is not using Perl to store the sequence etc. This interface defines what bioperl consideres necessary to "be" a sequence, without providing an implementation of this. (An implementation is provided in Bio::PrimarySeq). If you want to provide a Bio::PrimarySeq 'compliant' object which in fact wraps another object/database/out-of-perl experience, then this is the correct thing to wrap, generally by providing a wrapper class which would inheriet from your object and this Bio::PrimarySeqI interface. The wrapper class then would have methods lists in the "Implementation Specific Functions" which would provide these methods for your object. =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 - Ewan Birney Email birney@sanger.ac.uk =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::PrimarySeqI; use vars qw(@ISA ); use strict; use Bio::Root::RootI; use Bio::Tools::CodonTable; @ISA = qw(Bio::Root::RootI); =head1 Implementation Specific Functions These functions are the ones that a specific implementation must define. =head2 seq Title : seq Usage : $string = $obj->seq() Function: Returns the sequence as a string of letters. The case of the letters is left up to the implementer. Suggested cases are upper case for proteins and lower case for DNA sequence (IUPAC standard), but implementations are suggested to keep an open mind about case (some users... want mixed case!) Returns : A scalar Status : Virtual =cut sub seq { my ($self) = @_; $self->throw_not_implemented(); } =head2 subseq Title : subseq Usage : $substring = $obj->subseq(10,40); Function: returns the subseq from start to end, where the first base is 1 and the number is inclusive, ie 1-2 are the first two bases of the sequence Start cannot be larger than end but can be equal Returns : a string Args : Status : Virtual =cut sub subseq{ my ($self) = @_; $self->throw_not_implemented(); } =head2 display_id Title : display_id Usage : $id_string = $obj->display_id(); Function: returns the display id, aka the common name of the Sequence object. The semantics of this is that it is the most likely string to be used as an identifier of the sequence, and likely to have "human" readability. The id is equivalent to the ID field of the GenBank/EMBL databanks and the id field of the Swissprot/sptrembl database. In fasta format, the >(\S+) is presumed to be the id, though some people overload the id to embed other information. Bioperl does not use any embedded information in the ID field, and people are encouraged to use other mechanisms (accession field for example, or extending the sequence object) to solve this. Notice that $seq->id() maps to this function, mainly for legacy/convience issues Returns : A string Args : None Status : Virtual =cut sub display_id { my ($self) = @_; $self->throw_not_implemented(); } =head2 accession_number Title : accession_number Usage : $unique_biological_key = $obj->accession_number; Function: Returns the unique biological id for a sequence, commonly called the accession_number. For sequences from established databases, the implementors should try to use the correct accession number. Notice that primary_id() provides the unique id for the implemetation, allowing multiple objects to have the same accession number in a particular implementation. For sequences with no accession number, this method should return "unknown". Returns : A string Args : None Status : Virtual =cut sub accession_number { my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 primary_id Title : primary_id Usage : $unique_implementation_key = $obj->primary_id; Function: Returns the unique id for this object in this implementation. This allows implementations to manage their own object ids in a way the implementaiton can control clients can expect one id to map to one object. For sequences with no accession number, this method should return a stringified memory location. [Note this method name is likely to change in 1.3] Returns : A string Args : None Status : Virtual =cut sub primary_id { my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 can_call_new Title : can_call_new Usage : if( $obj->can_call_new ) { $newobj = $obj->new( %param ); } Function: can_call_new returns 1 or 0 depending on whether an implementation allows new constructor to be called. If a new constructor is allowed, then it should take the followed hashed constructor list. $myobject->new( -seq => $sequence_as_string, -display_id => $id -accession_number => $accession -alphabet => 'dna', ); Example : Returns : 1 or 0 Args : =cut sub can_call_new{ my ($self,@args) = @_; # we default to 0 here return 0; } =head2 alphabet Title : alphabet Usage : if( $obj->alphabet eq 'dna' ) { /Do Something/ } Function: Returns the type of sequence being one of 'dna', 'rna' or 'protein'. This is case sensitive. This is not called <type> because this would cause upgrade problems from the 0.5 and earlier Seq objects. Returns : a string either 'dna','rna','protein'. NB - the object must make a call of the type - if there is no type specified it has to guess. Args : none Status : Virtual =cut sub alphabet{ my ( $self ) = @_; $self->throw_not_implemented(); } sub moltype{ my ($self,@args) = @_; $self->warn("moltype: pre v1.0 method. Calling alphabet() instead..."); $self->alphabet(@args); } =head1 Optional Implementation Functions The following functions rely on the above functions. An implementing class does not need to provide these functions, as they will be provided by this class, but is free to override these functions. All of revcom(), trunc(), and translate() create new sequence objects. They will call new() on the class of the sequence object instance passed as argument, unless can_call_new() returns FALSE. In the latter case a Bio::PrimarySeq object will be created. Implementors which really want to control how objects are created (eg, for object persistence over a database, or objects in a CORBA framework), they are encouraged to override these methods =head2 revcom Title : revcom Usage : $rev = $seq->revcom() Function: Produces a new Bio::PrimarySeqI implementing object which is the reversed complement of the sequence. For protein sequences this throws an exception of "Sequence is a protein. Cannot revcom" The id is the same id as the original sequence, and the accession number is also indentical. If someone wants to track that this sequence has be reversed, it needs to define its own extensions To do an inplace edit of an object you can go: $seq = $seq->revcom(); This of course, causes Perl to handle the garbage collection of the old object, but it is roughly speaking as efficient as an inplace edit. Returns : A new (fresh) Bio::PrimarySeqI object Args : none =cut sub revcom{ my ($self) = @_; # check the type is good first. my $t = $self->alphabet; if( $t eq 'protein' ) { $self->throw("Sequence is a protein. Cannot revcom"); } if( $t ne 'dna' && $t ne 'rna' ) { if( $self->can('warn') ) { $self->warn("Sequence is not dna or rna, but [$t]. ". "Attempting to revcom, but unsure if this is right"); } else { warn("[$self] Sequence is not dna or rna, but [$t]. ". "Attempting to revcom, but unsure if this is right"); } } # yank out the sequence string my $str = $self->seq(); # if is RNA - map to DNA then map back if( $t eq 'rna' ) { $str =~ tr/uU/tT/; } # revcom etc... $str =~ tr/acgtrymkswhbvdnxACGTRYMKSWHBVDNX/tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX/; my $revseq = CORE::reverse $str; if( $t eq 'rna' ) { $revseq =~ tr/tT/uU/; } my $seqclass; if($self->can_call_new()) { $seqclass = ref($self); } else { $seqclass = 'Bio::PrimarySeq'; $self->_attempt_to_load_Seq(); } my $out = $seqclass->new( '-seq' => $revseq, '-display_id' => $self->display_id, '-accession_number' => $self->accession_number, '-alphabet' => $self->alphabet, '-desc' => $self->desc(), '-verbose' => $self->verbose ); return $out; } =head2 trunc Title : trunc Usage : $subseq = $myseq->trunc(10,100); Function: Provides a truncation of a sequence, Example : Returns : a fresh Bio::PrimarySeqI implementing object Args : Two integers denoting first and last base of the sub-sequence. =cut sub trunc{ my ($self,$start,$end) = @_; my $str; if( defined $start && ref($start) && $start->isa('Bio::LocationI') ) { $str = $self->subseq($start); # start is a location actually } elsif( !$end ) { $self->throw("trunc start,end -- there was no end for $start"); } elsif( $end < $start ) { my $msg = "start [$start] is greater than end [$end]. \n". "If you want to truncated and reverse complement, \n". "you must call trunc followed by revcom. Sorry."; $self->throw($msg); } else { $str = $self->subseq($start,$end); } my $seqclass; if($self->can_call_new()) { $seqclass = ref($self); } else { $seqclass = 'Bio::PrimarySeq'; $self->_attempt_to_load_Seq(); } my $out = $seqclass->new( '-seq' => $str, '-display_id' => $self->display_id, '-accession_number' => $self->accession_number, '-alphabet' => $self->alphabet, '-desc' => $self->desc(), '-verbose' => $self->verbose ); return $out; } =head2 translate Title : translate Usage : $protein_seq_obj = $dna_seq_obj->translate #if full CDS expected: $protein_seq_obj = $cds_seq_obj->translate(undef,undef,undef,undef,1); Function: Provides the translation of the DNA sequence using full IUPAC ambiguities in DNA/RNA and amino acid codes. The full CDS translation is identical to EMBL/TREMBL database translation. Note that the trailing terminator character is removed before returning the translation object. Note: if you set $dna_seq_obj->verbose(1) you will get a warning if the first codon is not a valid initiator. Returns : A Bio::PrimarySeqI implementing object Args : character for terminator (optional) defaults to '*' character for unknown amino acid (optional) defaults to 'X' frame (optional) valid values 0, 1, 2, defaults to 0 codon table id (optional) defaults to 1 complete coding sequence expected, defaults to 0 (false) boolean, throw exception if not complete CDS (true) or defaults to warning (false) coding sequence expected to be complete at 5', defaults to false coding sequence expected to be complete at 3', defaults to false =cut sub translate { my($self) = shift; my($stop, $unknown, $frame, $tableid, $fullCDS, $throw, $complete5, $complete3) = @_; my($i, $len, $output) = (0,0,''); my($codon) = ""; my $aa; ## User can pass in symbol for stop and unknown codons unless(defined($stop) and $stop ne '') { $stop = "*"; } unless(defined($unknown) and $unknown ne '') { $unknown = "X"; } unless(defined($frame) and $frame ne '') { $frame = 0; } ## the codon table ID unless(defined($tableid) and $tableid ne '') { $tableid = 1; } ##Error if monomer is "Amino" $self->throw("Can't translate an amino acid sequence.") if ($self->alphabet eq 'protein'); ##Error if frame is not 0, 1 or 2 $self->throw("Valid values for frame are 0, 1, 2, not [$frame].") unless ($frame == 0 or $frame == 1 or $frame == 2); #warns if ID is invalid my $codonTable = Bio::Tools::CodonTable->new( -id => $tableid); my ($seq) = $self->seq(); # deal with frame offset. if( $frame ) { $seq = substr ($seq,$frame); } # Translate it $output = $codonTable->translate($seq); # Use user-input stop/unknown $output =~ s/\*/$stop/g; $output =~ s/X/$unknown/g; # $complete5 and $complete3 indicate completeness of # the coding sequence at the 5' and 3' ends. Complete # if true, default to false. These are in addition to # $fullCDS, for backwards compatibility defined($complete5) or ($complete5 = $fullCDS ? 1 : 0); defined($complete3) or ($complete3 = $fullCDS ? 1 : 0); my $id = $self->display_id; # only if we are expecting to be complete at the 5' end if($complete5) { # if the initiator codon is not ATG, the amino acid needs to changed into M if(substr($output,0,1) ne 'M') { if($codonTable->is_start_codon(substr($seq, 0, 3)) ) { $output = 'M' . substr($output, 1); } elsif($throw) { $self->throw("Seq [$id]: Not using a valid initiator codon!"); } else { $self->warn("Seq [$id]: Not using a valid initiator codon!"); } } } # only if we are expecting to be complete at the 3' end if($complete3) { #remove the stop character if(substr($output, -1, 1) eq $stop) { chop $output; } else { $throw && $self->throw("Seq [$id]: Not using a valid terminator codon!"); $self->warn("Seq [$id]: Not using a valid terminator codon!"); } } # only if we are expecting to translate a complete coding region if($complete5 and $complete3) { # test if there are terminator characters inside the protein sequence! if($output =~ /\*/) { $throw && $self->throw("Seq [$id]: Terminator codon inside CDS!"); $self->warn("Seq [$id]: Terminator codon inside CDS!"); } } my $seqclass; if($self->can_call_new()) { $seqclass = ref($self); } else { $seqclass = 'Bio::PrimarySeq'; $self->_attempt_to_load_Seq(); } my $out = $seqclass->new( '-seq' => $output, '-display_id' => $self->display_id, '-accession_number' => $self->accession_number, # is there anything wrong with retaining the # description? '-desc' => $self->desc(), '-alphabet' => 'protein', '-verbose' => $self->verbose ); return $out; } =head2 id Title : id Usage : $id = $seq->id() Function: ID of the sequence. This should normally be (and actually is in the implementation provided here) just a synonym for display_id(). Example : Returns : A string. Args : =cut sub id { return shift->display_id(); } =head2 length Title : length Usage : $len = $seq->length() Function: Example : Returns : integer representing the length of the sequence. Args : =cut sub length { shift->throw_not_implemented(); } =head2 desc Title : desc Usage : $seq->desc($newval); $description = $seq->desc(); Function: Get/set description text for a seq object Example : Returns : value of desc Args : newvalue (optional) =cut sub desc { my ($self,$value) = @_; $self->throw_not_implemented(); } =head2 is_circular Title : is_circular Usage : if( $obj->is_circular) { /Do Something/ } Function: Returns true if the molecule is circular Returns : Boolean value Args : none =cut sub is_circular{ shift->throw_not_implemented(); } =head1 Private functions These are some private functions for the PrimarySeqI interface. You do not need to implement these functions =head2 _attempt_to_load_Seq Title : _attempt_to_load_Seq Usage : Function: Example : Returns : Args : =cut sub _attempt_to_load_Seq{ my ($self) = @_; if( $main::{'Bio::PrimarySeq'} ) { return 1; } else { eval { require Bio::PrimarySeq; }; if( $@ ) { my $text = "Bio::PrimarySeq could not be loaded for [$self]\n". "This indicates that you are using Bio::PrimarySeqI ". "without Bio::PrimarySeq loaded or without providing a ". "complete implementation.\nThe most likely problem is that there ". "has been a misconfiguration of the bioperl environment\n". "Actual exception:\n\n"; $self->throw("$text$@\n"); return 0; } return 1; } } 1;