Bio::PrimarySeqI.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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( $@ ) {
            $obj->throw("Could not reverse complement. ".
                     "Probably not DNA. Actual exception\n$@\n");
     }
 
     $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:
   http://bugzilla.open-bio.org/
 
 

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 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 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).
 
 

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_orf

  Title   : _find_orf
  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 nucleotide sequence or nothing, if no initiation codon is found.
  Args    : Nucleotide sequence, CodonTable object, alternative initiation
            codon (optional).
 
 

_attempt_to_load_Seq

  Title   : _attempt_to_load_Seq
  Usage   :
  Function:
  Example :
  Returns :
  Args    :