Bio::PrimarySeqI(3)

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:

  https://github.com/bioperl/bioperl-live/issues

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.

Implementation-optional 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 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

  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    :