BioSeq____perldoc

NAME
    Bio::Seq - Sequence object, with features
 
SYNOPSIS
        # This is the main sequence object in Bioperl
 
        # gets a sequence from a file
        # SeqIO can both read and write sequences; 
        $seqio  = Bio::SeqIO->new( '-format' => 'embl' , -file => 'myfile.dat');
        $seqobj = $seqio->next_seq();
 
        # get from database
        $db = Bio::DB::GenBank->new();
        $seqobj = $db->get_Seq_by_acc('X78121');
 
        # make from strings in script
        $seqobj = Bio::Seq->new( -display_id => 'my_id',
                                 -seq => $sequence_as_string);
 
        # gets sequence as a string from sequence object
        $seqstr   = $seqobj->seq(); # actual sequence as a string
        $seqstr   = $seqobj->subseq(10,50); # slice in biological coordinates
 
        # retrieves information from the sequence
        # features must implement Bio::SeqFeatureI interface
        @features = $seqobj->get_SeqFeatures(); # just top level
        foreach my $feat ( @features ) {
            print "Feature ",$feat->primary_tag," starts ",$feat->start," ends ",
            $feat->end," strand ",$feat->strand,"/n";
 
            # features retain link to underlying sequence object
            print "Feature sequence is ",$feat->seq->seq(),"/n"
        }
 
        # sequences may have a species
        if( defined $seq->species ) {
            print "Sequence is from ",$species->binomial," [",$species->common_name,"]/n";
        }
 
        # annotation objects are Bio::AnnotationCollectionI's
        $ann      = $seqobj->annotation(); # annotation object
 
        # references is one type of annotations to get. Also get
        # comment and dblink. Look at Bio::AnnotationCollection for
        # more information
 
        foreach my $ref ( $ann->get_Annotations('reference') ) {
            print "Reference ",$ref->title,"/n";
        }
 
        # you can get truncations, translations and reverse complements, these
        # all give back Bio::Seq objects themselves, though currently with no
        # features transfered
 
        my $trunc = $seqobj->trunc(100,200);
        my $rev   = $seqobj->revcom();
 
        # there are many options to translate - check out the docs
        my $trans = $seqobj->translate();
 
        # these functions can be chained together
 
        my $trans_trunc_rev = $seqobj->trunc(100,200)->revcom->translate();
 
DESCRIPTION
    A Seq object is a sequence with sequence features placed on it. The Seq
    object contains a PrimarySeq object for the actual sequence and also
    implements its interface.
 
    In Bioperl we have 3 main players that people are going to use
    frequently
 
      Bio::PrimarySeq  - just the sequence and its names, nothing else.
      Bio::SeqFeatureI - a feature on a sequence, potentially with a sequence
                         and a location and annotation.
      Bio::Seq         - A sequence and a collection of sequence features
                         (an aggregate) with its own annotation.
 
    Although Bioperl is not tied heavily to file formats these distinctions
    do map to file formats sensibly and for some bioinformaticians this
    might help
 
      Bio::PrimarySeq  - Fasta file of a sequence
      Bio::SeqFeatureI - A single entry in an EMBL/GenBank/DDBJ feature table
      Bio::Seq         - A single EMBL/GenBank/DDBJ entry
 
    By having this split we avoid a lot of nasty circular references
    (sequence features can hold a reference to a sequence without the
    sequence holding a reference to the sequence feature). See
    Bio::PrimarySeq and Bio::SeqFeatureI for more information.
 
    Ian Korf really helped in the design of the Seq and SeqFeature system.
 
  Examples
    This next script will take a file of sequences in EMBL format and create a file of the
    reverse-complemented sequences in Fasta format using Seq objects. It
    also prints out details about the exons it finds as sequence features in
    Genbank Flat File format.
 
      use Bio::Seq;
      use Bio::SeqIO;
 
      $seqin = Bio::SeqIO->new( -format => 'EMBL' , -file => 'myfile.dat');# create a SeqIO object
      $seqout= Bio::SeqIO->new( -format => 'Fasta', -file => '>output.fa');
 
      while((my $seqobj = $seqin->next_seq())) {                  # get a Seq object
          print "Seen sequence ",$seqobj->display_id,", start of seq ",
                substr($seqobj->seq,1,10),"/n";
          if( $seqobj->alphabet eq 'dna') {
                $rev = $seqobj->revcom;
                $id  = $seqobj->display_id();
                $id  = "$id.rev";
                $rev->display_id($id);
                $seqout->write_seq($rev);
          }
 
          foreach $feat ( $seqobj->get_SeqFeatures() ) {
               if( $feat->primary_tag eq 'exon' ) {
                  print STDOUT "Location ",$feat->start,":",
                        $feat->end," GFF[",$feat->gff_string,"]/n";
               }
          }
      }
 
    Let's examine the script. The lines below import the Bioperl modules.
    Seq is the main Bioperl sequence object and SeqIO is the Bioperl support
    for reading sequences from files and to files
 
      use Bio::Seq;
      use Bio::SeqIO;
 
    These two lines create two SeqIO streams: one for reading in sequences
    and one for outputting sequences:
 
      $seqin = Bio::SeqIO->new( -format => 'EMBL' , -file => 'myfile.dat');
      $seqout= Bio::SeqIO->new( -format => 'Fasta', -file => '>output.fa');
 
    Notice that in the "$seqout" case there is a greater-than sign,
    indicating the file is being opened for writing.
 
    Using the
 
      '-argument' => value
 
    syntax is common in Bioperl. The file argument is like an argument to
    open() . You can also pass in filehandles or FileHandle objects by using
    the -fh argument (see Bio::SeqIO documentation for details). Many
    formats in Bioperl are handled, including Fasta, EMBL, GenBank,
    Swissprot (swiss), PIR, and GCG.
 
      $seqin = Bio::SeqIO->new( -format => 'EMBL' , -file => 'myfile.dat');
      $seqout= Bio::SeqIO->new( -format => 'Fasta', -file => '>output.fa');
 
    This is the main loop which will loop progressively through sequences in
    a file, and each call to $seqio->next_seq() provides a new Seq object
    from the file:
 
      while((my $seqobj = $seqio->next_seq())) {
 
    This print line below accesses fields in the Seq object directly. The
    $seqobj->display_id is the way to access the display_id attribute of the
    Seq object. The $seqobj->seq method gets the actual sequence out as
    string. Then you can do manipulation of this if you want to (there are
    however easy ways of doing truncation, reverse-complement and
    translation).
 
      print "Seen sequence ",$seqobj->display_id,", start of seq ",
                   substr($seqobj->seq,1,10),"/n";
 
    Bioperl has to guess the alphabet of the sequence, being either 'dna',
    'rna', or 'protein'. The alphabet attribute is one of these three
    possibilities.
 
      if( $seqobj->alphabet eq 'dna') {
 
    The $seqobj->revcom method provides the reverse complement of the Seq
    object as another Seq object. Thus, the $rev variable is a reference to
    another Seq object. For example, one could repeat the above print line
    for this Seq object (putting $rev in place of $seqobj). In this case we
    are going to output the object into the file stream we built earlier on.
 
      $rev = $seqobj->revcom;
 
    When we output it, we want the id of the outputted object to be changed
    to "$id.rev", ie, with .rev on the end of the name. The following lines
    retrieve the id of the sequence object, add .rev to this and then set
    the display_id of the rev sequence object to this. Notice that to set
    the display_id attribute you just need call the same method,
    display_id(), with the new value as an argument. Getting and setting
    values with the same method is common in Bioperl.
 
      $id  = $seqobj->display_id();
      $id  = "$id.rev";
      $rev->display_id($id);
 
    The write_seq method on the SeqIO output object, $seqout, writes the
    $rev object to the filestream we built at the top of the script. The
    filestream knows that it is outputting in fasta format, and so it
    provides fasta output.
 
      $seqout->write_seq($rev);
 
    This block of code loops over sequence features in the sequence object,
    trying to find ones who have been tagged as 'exon'. Features have start
    and end attributes and can be outputted in Genbank Flat File format,
    GFF, a standarized format for sequence features.
 
      foreach $feat ( $seqobj->get_SeqFeatures() ) {
          if( $feat->primary_tag eq 'exon' ) {
              print STDOUT "Location ",$feat->start,":",
                 $feat->end," GFF[",$feat->gff_string,"]/n";
          }
      }
 
    The code above shows how a few Bio::Seq methods suffice to read, parse,
    reformat and analyze sequences from a file. A full list of methods
    available to Bio::Seq objects is shown below. Bear in mind that some of
    these methods come from PrimarySeq objects, which are simpler than Seq
    objects, stripped of features (see Bio::PrimarySeq for more
    information).
 
      # these methods return strings, and accept strings in some cases:
 
      $seqobj->seq();              # string of sequence
      $seqobj->subseq(5,10);       # part of the sequence as a string
      $seqobj->accession_number(); # when there, the accession number
      $seqobj->alphabet();         # one of 'dna','rna',or 'protein'
      $seqobj->seq_version()       # when there, the version
      $seqobj->keywords();         # when there, the Keywords line
      $seqobj->length()            # length
      $seqobj->desc();             # description
      $seqobj->primary_id();       # a unique id for this sequence regardless
                                   # of its display_id or accession number
      $seqobj->display_id();       # the human readable id of the sequence
 
    Some of these values map to fields in common formats. For example, The
    display_id() method returns the LOCUS name of a Genbank entry, the (/S+)
    following the > character in a Fasta file, the ID from a SwissProt file,
    and so on. The desc() method will return the DEFINITION line of a
    Genbank file, the description following the display_id in a Fasta file,
    and the DE field in a SwissProt file.
 
      # the following methods return new Seq objects, but
      # do not transfer features across to the new object:
 
      $seqobj->trunc(5,10)  # truncation from 5 to 10 as new object
      $seqobj->revcom       # reverse complements sequence
      $seqobj->translate    # translation of the sequence
 
      # if new() can be called this method returns 1, else 0
 
      $seqobj->can_call_new
 
      # the following method determines if the given string will be accepted
      # by the seq() method - if the string is acceptable then validate()
      # returns 1, or 0 if not
 
      $seqobj->validate_seq($string)
 
      # the following method returns or accepts a Species object:
 
      $seqobj->species();
 
    Please see Bio::Species for more information on this object.
 
      # the following method returns or accepts an Annotation object
      # which in turn allows access to Annotation::Reference
      # and Annotation::Comment objects:
 
      $seqobj->annotation();
 
    These annotations typically refer to entire sequences, unlike features.
    See Bio::AnnotationCollectionI, Bio::Annotation::Collection,
    Bio::Annotation::Reference, and Bio::Annotation::Comment for details.
 
    It is also important to be able to describe defined portions of a
    sequence. The combination of some description and the corresponding
    sub-sequence is called a feature - an exon and its coordinates within a
    gene is an example of a feature, or a domain within a protein.
 
      # the following methods return an array of SeqFeatureI objects:
 
      $seqobj->get_SeqFeatures # The 'top level' sequence features
      $seqobj->get_all_SeqFeatures # All sequence features, including sub-seq
                                   # features, such as features in an exon
 
      # to find out the number of features use:
 
      $seqobj->feature_count
 
    Here are just some of the methods available to SeqFeatureI objects:
 
      # these methods return numbers:
 
      $feat->start          # start position (1 is the first base)
      $feat->end            # end position (2 is the second base)
      $feat->strand         # 1 means forward, -1 reverse, 0 not relevant
 
      # these methods return or accept strings:
 
      $feat->primary_tag    # the name of the sequence feature, eg
                            # 'exon', 'glycoslyation site', 'TM domain'
      $feat->source_tag     # where the feature comes from, eg, 'EMBL_GenBank',
                            # or 'BLAST'
 
      # this method returns the more austere PrimarySeq object, not a
      # Seq object - the main difference is that PrimarySeq objects do not
      # themselves contain sequence features
 
      $feat->seq            # the sequence between start,end on the
                            # correct strand of the sequence
 
    See Bio::PrimarySeq for more details on PrimarySeq objects.
 
      # useful methods for feature comparisons, for start/end points
 
      $feat->overlaps($other)  # do $feat and $other overlap?
      $feat->contains($other)  # is $other completely within $feat?
      $feat->equals($other)    # do $feat and $other completely agree?
 
      # one can also add features
 
      $seqobj->add_SeqFeature($feat)     # returns 1 if successful
      $seqobj->add_SeqFeature(@features) # returns 1 if successful
 
      # sub features. For complex join() statements, the feature
      # is one sequence feature with many sub SeqFeatures
 
      $feat->sub_SeqFeature  # returns array of sub seq features
 
    Please see Bio::SeqFeatureI and Bio::SeqFeature::Generic, for more
    information on sequence features.
 
    It is worth mentioning that one can also retrieve the start and end
    positions of a feature using a Bio::LocationI object:
 
      $location = $feat->location # $location is a Bio::LocationI object
      $location->start;           # start position
      $location->end;             # end position
 
    This is useful because one needs a Bio::Location::SplitLocationI object
    in order to retrieve the coordinates inside the Genbank or EMBL join()
    statements (e.g. "CDS join(51..142,273..495,1346..1474)"):
 
      if ( $feat->location->isa('Bio::Location::SplitLocationI') &&
                   $feat->primary_tag eq 'CDS' )  {
        foreach $loc ( $feat->location->sub_Location ) {
          print $loc->start . ".." . $loc->end . "/n";
        }
      }
 
    See Bio::LocationI and Bio::Location::SplitLocationI for more
    information.
 
Implemented Interfaces
    This class implements the following interfaces.
 
    Bio::SeqI
        Note that this includes implementing Bio::PrimarySeqI.
 
    Bio::IdentifiableI
    Bio::DescribableI
    Bio::AnnotatableI
    Bio::FeatureHolderI
 
APPENDIX
    The rest of the documentation details each of the object methods.
    Internal methods are usually preceded with a "_".
 
  new
     Title   : new
     Usage   : $seq = Bio::Seq->new( -seq => 'ATGGGGGTGGTGGTACCCT',
                                     -id  => 'human_id',
                                     -accession_number => 'AL000012',
                                   );
 
     Function: Returns a new Seq object from
               basic constructors, being a string for the sequence
               and strings for id and accession_number
     Returns : a new Bio::Seq object
 
PrimarySeq interface
    The PrimarySeq interface provides the basic sequence getting and setting
    methods for on all sequences.
 
    These methods implement the Bio::PrimarySeq interface by delegating to
    the primary_seq inside the object. This means that you can use a Seq
    object wherever there is a PrimarySeq, and of course, you are free to
    use these functions anyway.
 
  seq
     Title   : seq
     Usage   : $string = $obj->seq()
     Function: Get/Set 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
     Args    : Optionally on set the new value (a string). An optional second
               argument presets the alphabet (otherwise it will be guessed).
               Both parameters may also be given in named paramater style
               with -seq and -alphabet being the names.
 
  validate_seq
     Title   : validate_seq
     Usage   : if(! $seq->validate_seq($seq_str) ) {
                    print "sequence $seq_str is not valid for an object of type ",
                          ref($seq), "/n";
               }
     Function: Validates a given sequence string. A validating sequence string
               must be accepted by seq(). A string that does not validate will
               lead to an exception if passed to seq().
 
               The implementation provided here does not take alphabet() into
               account. Allowed are all letters (A-Z), '-','.','*','=', and '~'.
 
     Example :
     Returns : 1 if the supplied sequence string is valid for the object, and
               0 otherwise.
     Args    : The sequence string to be validated.
 
  length
     Title   : length
     Usage   : $len = $seq->length()
     Function:
     Example :
     Returns : Integer representing the length of the sequence.
     Args    : None
 
Methods from the Bio::PrimarySeqI interface
  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    : 2 integers
 
  display_id
     Title   : display_id
     Usage   : $id = $obj->display_id or $obj->display_id($newid);
     Function: Gets or sets the display id, also known as the common name of
               the Seq 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 LOCUS
               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 issues.
     Returns : A string
     Args    : None or a new id
 
  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".
 
               Can also be used to set the accession number.
     Example : $key = $seq->accession_number or $seq->accession_number($key)
     Returns : A string
     Args    : None or an accession number
 
  desc
     Title   : desc
     Usage   : $seqobj->desc($string) or $seqobj->desc()
     Function: Sets or gets the description of the sequence
     Example :
     Returns : The description
     Args    : The description or none
 
  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 implementation can control
               clients can expect one id to map to one object.
 
               For sequences with no natural id, this method should return
               a stringified memory location.
 
               Can also be used to set the primary_id (or unset to undef).
 
               [Note this method name is likely to change in 1.3]
 
     Example : $id = $seq->primary_id or $seq->primary_id($id)
     Returns : A string
     Args    : None or an id, or undef to unset the primary id.
 
  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    : None
 
  alphabet
     Title   : alphabet
     Usage   : if ( $obj->alphabet eq 'dna' ) { /Do Something/ }
     Function: Get/Set 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    : optional string to set : 'dna' | 'rna' | 'protein'
 
  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
 
Methods for Bio::IdentifiableI compliance
  object_id
     Title   : object_id
     Usage   : $string    = $obj->object_id()
     Function: a string which represents the stable primary identifier
               in this namespace of this object. For DNA sequences this
               is its accession_number, similarly for protein sequences
 
               This is aliased to accession_number().
     Returns : A scalar
 
  version
     Title   : version
     Usage   : $version    = $obj->version()
     Function: a number which differentiates between versions of
               the same object. Higher numbers are considered to be
               later and more relevant, but a single object described
               the same identifier should represent the same concept
 
     Returns : A number
 
  authority
     Title   : authority
     Usage   : $authority    = $obj->authority()
     Function: a string which represents the organisation which
               granted the namespace, written as the DNS name for
               organisation (eg, wormbase.org)
 
     Returns : A scalar
 
  namespace
     Title   : namespace
     Usage   : $string    = $obj->namespace()
     Function: A string representing the name space this identifier
               is valid in, often the database name or the name
               describing the collection
 
     Returns : A scalar
 
Methods for Bio::DescribableI compliance
  display_name
     Title   : display_name
     Usage   : $string    = $obj->display_name()
     Function: A string which is what should be displayed to the user
               the string should have no spaces (ideally, though a cautious
               user of this interface would not assumme this) and should be
               less than thirty characters (though again, double checking
               this is a good idea)
 
               This is aliased to display_id().
     Returns : A scalar
 
  description
     Title   : description
     Usage   : $string    = $obj->description()
     Function: A text string suitable for displaying to the user a
               description. This string is likely to have spaces, but
               should not have any newlines or formatting - just plain
               text. The string should not be greater than 255 characters
               and clients can feel justified at truncating strings at 255
               characters for the purposes of display
 
               This is aliased to desc().
     Returns : A scalar
 
Methods for implementing Bio::AnnotatableI
  annotation
     Title   : annotation
     Usage   : $ann = $seq->annotation or 
               $seq->annotation($ann)
     Function: Gets or sets the annotation
     Returns : Bio::AnnotationCollectionI object
     Args    : None or Bio::AnnotationCollectionI object
 
    See Bio::AnnotationCollectionI and Bio::Annotation::Collection for more
    information
 
Methods to implement Bio::FeatureHolderI
    This includes methods for retrieving, adding, and removing features.
 
  get_SeqFeatures
     Title   : get_SeqFeatures
     Usage   :
     Function: Get the feature objects held by this feature holder.
 
               Features which are not top-level are subfeatures of one or
               more of the returned feature objects, which means that you
               must traverse the subfeature arrays of each top-level
               feature object in order to traverse all features associated
               with this sequence.
 
               Use get_all_SeqFeatures() if you want the feature tree
               flattened into one single array.
 
     Example :
     Returns : an array of Bio::SeqFeatureI implementing objects
     Args    : none
 
    At some day we may want to expand this method to allow for a feature
    filter to be passed in.
 
  get_all_SeqFeatures
     Title   : get_all_SeqFeatures
     Usage   : @feat_ary = $seq->get_all_SeqFeatures();
     Function: Returns the tree of feature objects attached to this
               sequence object flattened into one single array. Top-level
               features will still contain their subfeature-arrays, which
               means that you will encounter subfeatures twice if you
               traverse the subfeature tree of the returned objects.
 
               Use get_SeqFeatures() if you want the array to contain only
               the top-level features.
 
     Returns : An array of Bio::SeqFeatureI implementing objects.
     Args    : None
 
  feature_count
     Title   : feature_count
     Usage   : $seq->feature_count()
     Function: Return the number of SeqFeatures attached to a sequence
     Returns : integer representing the number of SeqFeatures
     Args    : None
 
  add_SeqFeature
     Title   : add_SeqFeature
     Usage   : $seq->add_SeqFeature($feat);
               $seq->add_SeqFeature(@feat);
     Function: Adds the given feature object (or each of an array of feature
               objects to the feature array of this
               sequence. The object passed is required to implement the
               Bio::SeqFeatureI interface.
     Returns : 1 on success
     Args    : A Bio::SeqFeatureI implementing object, or an array of such objects.
 
  remove_SeqFeatures
     Title   : remove_SeqFeatures
     Usage   : $seq->remove_SeqFeatures();
     Function: Flushes all attached SeqFeatureI objects.
 
               To remove individual feature objects, delete those from the returned
               array and re-add the rest.
     Example :
     Returns : The array of Bio::SeqFeatureI objects removed from this seq.
     Args    : None
 
Methods provided in the Bio::PrimarySeqI interface
    These methods are inherited from the PrimarySeq interface and work as
    one expects, building new Bio::Seq objects or other information as
    expected. See Bio::PrimarySeq for more information.
 
    Sequence Features are not transfered to the new objects. This is
    possibly a mistake. Anyone who feels the urge in dealing with this is
    welcome to give it a go.
 
  revcom
     Title   : revcom
     Usage   : $rev = $seq->revcom()
     Function: Produces a new Bio::Seq 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 identical. If someone wants to track
               that this sequence has be reversed, it needs to define its own
               extensions
 
               To do an in-place 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
               in-place edit.
 
     Returns : A new (fresh) Bio::Seq object
     Args    : None
 
  trunc
     Title   : trunc
     Usage   : $subseq = $myseq->trunc(10,100);
     Function: Provides a truncation of a sequence
 
     Example :
     Returns : A fresh Seq object
     Args    : A Seq object
 
  id
     Title   : id
     Usage   : $id = $seq->id()
     Function: This is mapped on display_id
     Returns : value of display_id()
     Args    : [optional] value to update display_id
 
Seq only methods
    These methods are specific to the Bio::Seq object, and not found on the
    Bio::PrimarySeq object
 
  primary_seq
     Title   : primary_seq
     Usage   : $seq->primary_seq or $seq->primary_seq($newval)
     Function: Get or set a PrimarySeq object
     Example :
     Returns : PrimarySeq object
     Args    : None or PrimarySeq object
 
  species
     Title   : species
     Usage   : $species = $seq->species() or $seq->species($species)
     Function: Gets or sets the species
     Returns : L<Bio::Species> object
     Args    : None or L<Bio::Species> object
 
    See Bio::Species for more information
 
Internal methods