Bio::SeqFeatureI(3pm)

NAME

Bio::SeqFeatureI - Abstract interface of a Sequence Feature

SYNOPSIS

    # 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();
    }

DESCRIPTION

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 implementation, it just provides the definitions of what methods one can call. See Bio::SeqFeature::Generic for a good standard implementation of this object

FEEDBACK

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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

APPENDIX

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.

get_SeqFeatures

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

display_name

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

primary_tag

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

source_tag

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

has_tag

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

get_tag_values

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

throws an exception if there is no such tag

get_tagset_values

 Title   : get_tagset_values
 Usage   : @values = $self->get_tagset_values(qw(label transcript_id product))
 Function:
 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

get_all_tags

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

attach_seq

 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

seq

 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.
           If the strand is defined and set to -1, the returned sequence is
           the reverse-complement of the region
 Args    : none

entire_seq

 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

seq_id

 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)

gff_string

 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().

_static_gff_formatter

 Title   : _static_gff_formatter
 Usage   :
 Function:
 Example :
 Returns :
 Args    :

Decorating methods

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

spliced_seq

  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
            join(AB000123:5567-5589,80..1144)
            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

location

 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

primary_id

 Title   : primary_id
 Usage   : $obj->primary_id($newval)
 Function:
 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'

phase

 Title   : phase
 Usage   : $obj->phase($newval)
 Function: get/set this feature's phase.
 Example :
 Returns : undef if no phase is set,
           otherwise 0, 1, or 2 (the only valid values for phase)
 Args    : on set, the new value

Most features do not have or need a defined phase.

For features representing a CDS, the phase indicates where the feature begins with reference to the reading frame. The phase is one of the integers 0, 1, or 2, indicating the number of bases that should be removed from the beginning of this feature to reach the first base of the next codon. In other words, a phase of "0" indicates that the next codon begins at the first base of the region described by the current line, a phase of "1" indicates that the next codon begins at the second base of this region, and a phase of "2" indicates that the codon begins at the third base of this region. This is NOT to be confused with the frame, which is simply start modulo 3.

For forward strand features, phase is counted from the start field. For reverse strand features, phase is counted from the end field.

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).

start()

 See L<Bio::RangeI>

end()

 See L<Bio::RangeI>

strand()

 See L<Bio::RangeI>

overlaps()

 See L<Bio::RangeI>

contains()

 See L<Bio::RangeI>

equals()

 See L<Bio::RangeI>

intersection()

 See L<Bio::RangeI>

union()

 See L<Bio::RangeI>