Bio::Seq.3pm

Langue: en

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

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Seq - Sequence object, with features

SYNOPSIS

     # This is the main sequence object in Bioperl
 
     # gets a sequence from a file
     $seqio  = Bio::SeqIO->new( '-format' => 'embl' , -file => 'myfile.dat');
     $seqobj = $seqio->next_seq();
 
     # SeqIO can both read and write sequences; see Bio::SeqIO
     # for more information and examples
 
     # 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

A simple and fundamental block of code:
   use Bio::SeqIO;
 
   my $seqIOobj = Bio::SeqIO->new(-file=>"1.fa"); # create a SeqIO object
   my $seqobj = $seqIOobj->next_seq;              # get a Seq object
 
 

With the Seq object in hand one has access to a powerful set of Bioperl methods and related Bioperl objects. 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');
   $seqout= Bio::SeqIO->new( -format => 'Fasta', -file => '>output.fa');
 
   while((my $seqobj = $seqin->next_seq())) {
       print "Seen sequence ",$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

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, inspired by Ian Korf objects

Email birney@ebi.ac.uk

CONTRIBUTORS

Jason Stajich <jason@bioperl.org>

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