Langue: en

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

Section: 3 (Bibliothèques de fonctions)


Bio::SeqFeatureI - Abstract interface of a Sequence Feature


     # get a seqfeature somehow, eg, from a Sequence with Features attached
     foreach $feat ( $seq->get_SeqFeatures() ) {
        print "Feature from ", $feat->start, "to ",
                $feat->end, " Primary tag  ", $feat->primary_tag,
                   ", produced by ", $feat->source_tag(), "\n";
        if( $feat->strand == 0 ) {
                     print "Feature applicable to either strand\n";
        } else {
           print "Feature on strand ", $feat->strand,"\n"; # -1,1
        print "feature location is ",$feat->start, "..",
           $feat->end, " on strand ", $feat->strand, "\n";
        print "easy utility to print locations in GenBank/EMBL way ",
           $feat->location->to_FTstring(), "\n";
        foreach $tag ( $feat->get_all_tags() ) {
                     print "Feature has tag ", $tag, " with values, ",
                       join(' ',$feat->get_tag_values($tag)), "\n";
             print "new feature\n" if $feat->has_tag('new');
             # features can have sub features
             my @subfeat = $feat->get_SeqFeatures();


This interface is the functions one can expect for any Sequence Feature, whatever its implementation or whether it is a more complex type (eg, a Gene). This object does not actually provide any implemention, it just provides the definitions of what methods one can call. See Bio::SeqFeature::Generic for a good standard implementation of this object


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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

Bio::SeqFeatureI specific methods

New method interfaces.


  Title   : get_SeqFeatures
  Usage   : @feats = $feat->get_SeqFeatures();
  Function: Returns an array of sub Sequence Features
  Returns : An array
  Args    : none


  Title   : display_name
  Usage   : $name = $feat->display_name()
  Function: Returns the human-readable name of the feature for displays.
  Returns : a string
  Args    : none


  Title   : primary_tag
  Usage   : $tag = $feat->primary_tag()
  Function: Returns the primary tag for a feature,
            eg 'exon'
  Returns : a string
  Args    : none


  Title   : source_tag
  Usage   : $tag = $feat->source_tag()
  Function: Returns the source tag for a feature,
            eg, 'genscan'
  Returns : a string
  Args    : none


  Title   : has_tag
  Usage   : $tag_exists = $self->has_tag('some_tag')
  Returns : TRUE if the specified tag exists, and FALSE otherwise
  Args    :


  Title   : get_tag_values
  Usage   : @values = $self->get_tag_values('some_tag')
  Returns : An array comprising the values of the specified tag.
  Args    : a string

throws an exception if there is no such tag


  Title   : get_tagset_values
  Usage   : @values = $self->get_tagset_values(qw(label transcript_id product))
  Returns : An array comprising the values of the specified tags, in order of tags
  Args    : An array of strings

does NOT throw an exception if none of the tags are not present

this method is useful for getting a human-readable label for a SeqFeatureI; not all tags can be assumed to be present, so a list of possible tags in preferential order is provided


  Title   : get_all_tags
  Usage   : @tags = $feat->get_all_tags()
  Function: gives all tags for this feature
  Returns : an array of strings
  Args    : none


  Title   : attach_seq
  Usage   : $sf->attach_seq($seq)
  Function: Attaches a Bio::Seq object to this feature. This
            Bio::Seq object is for the *entire* sequence: ie
            from 1 to 10000
            Note that it is not guaranteed that if you obtain a feature from
            an object in bioperl, it will have a sequence attached. Also,
            implementors of this interface can choose to provide an empty
            implementation of this method. I.e., there is also no guarantee
            that if you do attach a sequence, seq() or entire_seq() will not
            return undef.
            The reason that this method is here on the interface is to enable
            you to call it on every SeqFeatureI compliant object, and
            that it will be implemented in a useful way and set to a useful
            value for the great majority of use cases. Implementors who choose
            to ignore the call are encouraged to specifically state this in
            their documentation.
  Example :
  Returns : TRUE on success
  Args    : a Bio::PrimarySeqI compliant object


  Title   : seq
  Usage   : $tseq = $sf->seq()
  Function: returns the truncated sequence (if there is a sequence attached)
            for this feature
  Example :
  Returns : sub seq (a Bio::PrimarySeqI compliant object) on attached sequence
            bounded by start & end, or undef if there is no sequence attached
  Args    : none


  Title   : entire_seq
  Usage   : $whole_seq = $sf->entire_seq()
  Function: gives the entire sequence that this seqfeature is attached to
  Example :
  Returns : a Bio::PrimarySeqI compliant object, or undef if there is no
            sequence attached
  Args    : none


  Title   : seq_id
  Usage   : $obj->seq_id($newval)
  Function: There are many cases when you make a feature that you
            do know the sequence name, but do not know its actual
            sequence. This is an attribute such that you can store
            the ID (e.g., display_id) of the sequence.
            This attribute should *not* be used in GFF dumping, as
            that should come from the collection in which the seq
            feature was found.
  Returns : value of seq_id
  Args    : newvalue (optional)


  Title   : gff_string
  Usage   : $str = $feat->gff_string;
            $str = $feat->gff_string($gff_formatter);
  Function: Provides the feature information in GFF format.
            The implementation provided here returns GFF2 by default. If you
            want a different version, supply an object implementing a method
            gff_string() accepting a SeqFeatureI object as argument. E.g., to
            obtain GFF1 format, do the following:
                 my $gffio = Bio::Tools::GFF->new(-gff_version => 1);
                 $gff1str = $feat->gff_string($gff1io);
  Returns : A string
  Args    : Optionally, an object implementing gff_string().


  Title   : _static_gff_formatter
  Usage   :
  Example :
  Returns :
  Args    :

Decorating methods

These methods have an implementation provided by Bio::SeqFeatureI, but can be validly overwritten by subclasses


   Title   : spliced_seq
   Usage   : $seq = $feature->spliced_seq()
             $seq = $feature_with_remote_locations->spliced_seq($db_for_seqs)
   Function: Provides a sequence of the feature which is the most
             semantically "relevant" feature for this sequence. A default
             implementation is provided which for simple cases returns just
             the sequence, but for split cases, loops over the split location
             to return the sequence. In the case of split locations with
             remote locations, eg
             in the case when a database object is passed in, it will attempt
             to retrieve the sequence from the database object, and "Do the right thing",
             however if no database object is provided, it will generate the correct
             number of N's (DNA) or X's (protein, though this is unlikely).
             This function is deliberately "magical" attempting to second guess
             what a user wants as "the" sequence for this feature.
             Implementing classes are free to override this method with their
             own magic if they have a better idea what the user wants.
   Args    : [optional]
             -db        A L<Bio::DB::RandomAccessI> compliant object if
                        one needs to retrieve remote seqs.
             -nosort    boolean if the locations should not be sorted
                        by start location.  This may occur, for instance,
                        in a circular sequence where a gene span starts
                        before the end of the sequence and ends after the
                        sequence start. Example : join(15685..16260,1..207)
                                            (default = if sequence is_circular(), 1, otherwise 0)
                         -phase     truncates the returned sequence based on the
                                            intron phase (0,1,2).
   Returns : A L<Bio::PrimarySeqI> object


  Title   : location
  Usage   : my $location = $seqfeature->location()
  Function: returns a location object suitable for identifying location
            of feature on sequence or parent feature
  Returns : Bio::LocationI object
  Args    : none


  Title   : primary_id
  Usage   : $obj->primary_id($newval)
  Example :
  Returns : value of primary_id (a scalar)
  Args    : on set, new value (a scalar or undef, optional)

Primary ID is a synonym for the tag 'ID'

Bio::RangeI methods

These methods are inherited from RangeI and can be used directly from a SeqFeatureI interface. Remember that a SeqFeature is-a RangeI, and so wherever you see RangeI you can use a feature ($r in the below documentation).


  See L<Bio::RangeI>


  See L<Bio::RangeI>


  See L<Bio::RangeI>


  See L<Bio::RangeI>


  See L<Bio::RangeI>


  See L<Bio::RangeI>


  See L<Bio::RangeI>


  See L<Bio::RangeI>