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bio::primaryseqi(3pm) [debian man page]

Bio::PrimarySeqI(3pm)					User Contributed Perl Documentation				     Bio::PrimarySeqI(3pm)

NAME
Bio::PrimarySeqI - Interface definition for a Bio::PrimarySeq SYNOPSIS
# Bio::PrimarySeqI is the interface class for sequences. # If you are a newcomer to bioperl, you might want to start with # Bio::Seq documentation. # Test if 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 $@ "); } $trunc = $obj->trunc(12,50); # $rev and $trunc are Bio::PrimarySeqI compliant objects 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 considers 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 inherit 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. FEEDBACK
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://bioperl.org/wiki/Mailing_lists - About the mailing lists Support Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. 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 the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Ewan Birney Email birney@ebi.ac.uk APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ Implementation Specific Functions These functions are the ones that a specific implementation must define. 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 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 : Status : Virtual 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 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 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 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', ); Returns : 1 or 0 Args : 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 alphabet, if there is no alphabet specified it has to guess. Args : None Status : Virtual moltype Title : moltype Usage : Deprecated. Use alphabet() instead. 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. 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 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 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. translate Title : translate Usage : $protein_seq_obj = $dna_seq_obj->translate Or if you expect a complete coding sequence (CDS) translation, with initiator 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 '*' -unknown character for unknown, default 'X' -frame positive integer frame shift (in bases), default 0 -codontable_id integer codon table id, default 1 -complete boolean, if true, complete CDS is expected. default false -complete_codons boolean, if true, codons which are incomplete are translated if a suitable amino acid is found. For instance, if the incomplete codon is 'GG', the completed codon is 'GGN', which is glycine (G). Defaults to 'false'; setting '-complete' also makes this true. -throw boolean, throw exception if ORF not complete, default false -orf if 'longest', find longest ORF. other true value, find first ORF. default 0 -codontable optional L<Bio::Tools::CodonTable> object to use for translation -start optional three-character string to force as initiation codon (e.g. 'atg'). If unset, start codons are determined by the CodonTable. Case insensitive. -offset optional positive integer offset for fuzzy locations. if set, must be either 1, 2, or 3 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 Bio::Tools::CodonTable. 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). transcribe() Title : transcribe Usage : $xseq = $seq->transcribe Function: Convert base T to base U Returns : PrimarySeqI object of alphabet 'rna' or undef if $seq->alphabet ne 'dna' Args : rev_transcribe() Title : rev_transcribe Usage : $rtseq = $seq->rev_transcribe Function: Convert base U to base T Returns : PrimarySeqI object of alphabet 'dna' or undef if $seq->alphabet ne 'rna' Args : 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 : length Title : length Usage : $len = $seq->length() Function: Returns : Integer representing the length of the sequence. Args : desc 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) 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 Private functions These are some private functions for the PrimarySeqI interface. You do not need to implement these functions _find_orfs_nucleotide Title : _find_orfs_nucleotide Usage : Function: Finds ORF starting at 1st initiation codon in nucleotide sequence. The ORF is not required to have a termination codon. Example : Returns : a list of string coordinates of ORF locations (0-based half-open), sorted descending by length (so that the longest is first) as: [ start, end, frame, length ], [ start, end, frame, length ], ... Args : Nucleotide sequence, CodonTable object, (optional) alternative initiation codon (e.g. 'ATA'), (optional) boolean that, if true, stops after finding the first available ORF _attempt_to_load_Seq Title : _attempt_to_load_Seq Usage : Function: Example : Returns : Args : perl v5.14.2 2012-03-02 Bio::PrimarySeqI(3pm)
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