/ 
BioPerl-1.007001
River stage two • 60 direct dependents • 65 total dependents
/ Bio::SeqFeatureI

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.

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

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>