role Bio::PrimarySeqI; # for alphabet, maybe switch to enum or a symbol class? #our subset Bio::Alphabet of Str where { $_ eq 'dna' | 'rna' | 'protein' }; has $.seq is rw; has $.display_id is rw; has $.description is rw; has $.accession_number is rw; has $.primary_id is rw; has $.display_id is rw; has Str $.alphabet is rw = 'dna'; has Bool $.is_circular is rw = Bool::False; =begin Functions =head1 Implementation Specific Functions These functions are the ones that a specific implementation must define. =end Functions =begin 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 =end seq =begin 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, i.e. 1-2 are the first two bases of the sequence. Start cannot be larger than end but can be equal. Returns : A string Args : start : sequence start end : sequence end relative : boolean flag indicating the positions are relative to sequence start/end no_gaps : if sequence has gap characters, removes them Status : Virtual =end subseq method subseq{ ... } =begin display_id Title : display_id Usage : $id_string = $obj.display_id; Function: Returns the display id, also known as 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/convenience reasons. Returns : A string Args : None Status : Virtual =end display_id =begin 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 =end accession_number =begin 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. Returns : A string Args : None Status : Virtual =end primary_id =begin 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. Returns : A string, either 'dna','rna','protein'. NB - the object must make a call of the alphabet, if there is no alphabet specified it has to guess. Args : None Status : Virtual =end alphabet =begin Optional =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. Care must be taken The revcom(), trunc(), and translate() methods 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. =end Optional =begin 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(). Returns : A string. Args : =end id method id { return self.display_id; } =begin 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 extensionsj. 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 =end revcom method revcom{ ... } =begin trunc Title : trunc Usage : $subseq = $myseq.trunc(10,100); Function: Provides a truncation of a sequence. Returns : A fresh Bio::PrimarySeqI implementing object. Args : Two integers denoting first and last base of the sub-sequence. =end trunc method trunc{ ... } =begin translate Title : translate Usage : $protein_seq_obj = $dna_seq_obj.translate Or if you expect a complete coding sequence (CDS) translation, with inititator at the beginning and terminator at the end: $protein_seq_obj = $cds_seq_obj.translate(-complete => 1); Or if you want translate() to find the first initiation codon and return the corresponding protein: $protein_seq_obj = $cds_seq_obj.translate(-orf => 1); Function: Provides the translation of the DNA sequence using full IUPAC ambiguities in DNA/RNA and amino acid codes. The complete CDS translation is identical to EMBL/TREMBL database translation. Note that the trailing terminator character is removed before returning the translated protein 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 : terminator - character for terminator default is * unknown - character for unknown default is X frame - frame default is 0 codontable_id - codon table id default is 1 complete - complete CDS expected default is 0 throw - throw exception if not complete default is 0 orf - find 1st ORF default is 0 start - alternative initiation codon codontable - Bio::Tools::CodonTable object offset - offset for fuzzy locations default is 0 Notes : The -start argument only applies when -orf is set to 1. By default all initiation codons found in the given codon table are used but when "start" is set to some codon this codon will be used exclusively as the initiation codon. Note that the default codon table (NCBI "Standard") has 3 initiation codons! By default translate() translates termination codons to the some character (default is *), both internal and trailing codons. Setting "-complete" to 1 tells translate() to remove the trailing character. -offset is used for seqfeatures which contain the the \codon_start tag and can be set to 1, 2, or 3. This is the offset by which the sequence translation starts relative to the first base of the feature For details on codon tables used by translate() see L. Deprecated argument set (v. 1.5.1 and prior versions) where each argument is an element in an array: 1: character for terminator (optional), defaults to '*'. 2: character for unknown amino acid (optional), defaults to 'X'. 3: frame (optional), valid values are 0, 1, 2, defaults to 0. 4: codon table id (optional), defaults to 1. 5: complete coding sequence expected, defaults to 0 (false). 6: boolean, throw exception if not complete coding sequence (true), defaults to warning (false) 7: codontable, a custom Bio::Tools::CodonTable object (optional). =end translate method translate { ... } =begin length Title : length Usage : $len = $seq.length() Function: Returns : Integer representing the length of the sequence. Args : =end length method length { return self.seq.length; } =begin description Title : desc Usage : $seq.desc = $newval; $description = $seq.desc(); Function: Get/set description text for a seq object Returns : Value of desc Args : newvalue (optional) =end description =begin 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 =end is_circular