Bio SeqFeatureI
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::SeqFeatureI - Abstract interface of a Sequence Feature
Package variables
Privates (from "my" definitions)
$static_gff_formatter = undef
Included modules
Bio::Seq
Carp
Inherit
Bio::AnnotatableI Bio::RangeI
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
implemention, it just provides the definitions of what methods one can
call. See Bio::SeqFeature::Generic for a good standard implementation
of this object
Methods
BEGIN Code
get_SeqFeaturesDescriptionCode
display_nameDescriptionCode
primary_tagDescriptionCode
source_tagDescriptionCode
attach_seqDescriptionCode
seqDescriptionCode
entire_seqDescriptionCode
seq_idDescriptionCode
gff_stringDescriptionCode
_static_gff_formatterDescriptionCode
spliced_seqDescriptionCode
locationDescriptionCode
primary_idDescriptionCode
generate_unique_persistent_id
No description
Code
Methods description
get_SeqFeaturescode    nextTop
 Title   : get_SeqFeatures
 Usage   : @feats = $feat->get_SeqFeatures();
 Function: Returns an array of sub Sequence Features
 Returns : An array
 Args    : none
display_namecodeprevnextTop
 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_tagcodeprevnextTop
 Title   : primary_tag
 Usage   : $tag = $feat->primary_tag()
 Function: Returns the primary tag for a feature,
           eg 'exon'
 Returns : a string
 Args    : none
source_tagcodeprevnextTop
 Title   : source_tag
 Usage   : $tag = $feat->source_tag()
 Function: Returns the source tag for a feature,
           eg, 'genscan'
 Returns : a string
 Args    : none
attach_seqcodeprevnextTop
 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
seqcodeprevnextTop
 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
entire_seqcodeprevnextTop
 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_idcodeprevnextTop
 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_stringcodeprevnextTop
 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_formattercodeprevnextTop
 Title   : _static_gff_formatter
 Usage   :
 Function:
 Example :
 Returns :
 Args    :
spliced_seqcodeprevnextTop
  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 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)
  Returns : A Bio::PrimarySeqI object
locationcodeprevnextTop
 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_idcodeprevnextTop
 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'
Methods code
BEGINTop
BEGIN {
    eval { require Bio::DB::InMemoryCache };
    if( $@ ) { $HasInMemory = 0 }
    else { $HasInMemory = 1
}
get_SeqFeaturesdescriptionprevnextTop
sub get_SeqFeatures {
   my ($self,@args) = @_;

   $self->throw_not_implemented();
}
display_namedescriptionprevnextTop
sub display_name {
    shift->throw_not_implemented();
}
primary_tagdescriptionprevnextTop
sub primary_tag {
   my ($self,@args) = @_;

   $self->throw_not_implemented();
}
source_tagdescriptionprevnextTop
sub source_tag {
   my ($self,@args) = @_;

   $self->throw_not_implemented();
}
attach_seqdescriptionprevnextTop
sub attach_seq {
    shift->throw_not_implemented();
}
seqdescriptionprevnextTop
sub seq {
    shift->throw_not_implemented();
}
entire_seqdescriptionprevnextTop
sub entire_seq {
    shift->throw_not_implemented();
}
seq_iddescriptionprevnextTop
sub seq_id {
    shift->throw_not_implemented();
}
gff_stringdescriptionprevnextTop
sub gff_string {
   my ($self,$formatter) = @_;

   $formatter = $self->_static_gff_formatter unless $formatter;
   return $formatter->gff_string($self);
}
_static_gff_formatterdescriptionprevnextTop
sub _static_gff_formatter {
   my ($self,@args) = @_;

   if( !defined $static_gff_formatter ) {
       $static_gff_formatter = Bio::Tools::GFF->new('-gff_version' => 2);
   }
   return $static_gff_formatter;
}
spliced_seqdescriptionprevnextTop
sub spliced_seq {
    my $self = shift;
	my @args = @_;
	my ($db,$nosort) = $self->_rearrange([qw(DB NOSORT)], @args);

	# (added 7/7/06 to allow use old API (with warnings)
	my $old_api = (!(grep {$_ =~ /(?:nosort|db)/} @args)) ? 1 : 0;
	if (@args && $old_api) {
		$self->warn(q(API has changed; please use '-db' or '-nosort' ).
                     qq(for args. See POD for more details.));
		$db = shift @args if @args;
		$nosort = shift @args if @args;
	};

	if( $db && ref($db) && ! $db->isa('Bio::DB::RandomAccessI') ) {
        $self->warn("Must pass in a valid Bio::DB::RandomAccessI object".
                    " for access to remote locations for spliced_seq");
        $db = undef;
    } elsif( defined $db && $HasInMemory &&
            $db->isa('Bio::DB::InMemoryCache') ) {
        $db = new Bio::DB::InMemoryCache(-seqdb => $db);
    }

    if( ! $self->location->isa("Bio::Location::SplitLocationI") ) {
	return $self->seq(); # nice and easy!
    }

    # redundant test, but the above ISA is probably not ideal.
    if( ! $self->location->isa("Bio::Location::SplitLocationI") ) {
	$self->throw("not atomic, not split, yikes, in trouble!");
    }

    my $seqstr = '';
    my $seqid = $self->entire_seq->display_id;
    # This is to deal with reverse strand features
    # so we are really sorting features 5' -> 3' on their strand
    # i.e. rev strand features will be sorted largest to smallest
    # as this how revcom CDSes seem to be annotated in genbank.
    # Might need to eventually allow this to be programable?
    # (can I mention how much fun this is NOT! --jason)

    my ($mixed,$mixedloc, $fstrand) = (0);

    if( $self->isa('Bio::Das::SegmentI') &&
	! $self->absolute ) {
	$self->warn("Calling spliced_seq with a Bio::Das::SegmentI which does have absolute set to 1 -- be warned you may not be getting things on the correct strand");
    }

    my @locset = $self->location->each_Location;
    my @locs;
    if( ! $nosort ) {
	@locs = map { $_->[0] }
	# sort so that most negative is first basically to order
	# the features on the opposite strand 5'->3' on their strand
	# rather than they way most are input which is on the fwd strand

	sort { $a->[1] <=> $b->[1] } # Yes Tim, Schwartzian transformation
	map {
	    $fstrand = $_->strand unless defined $fstrand;
	    $mixed = 1 if defined $_->strand && $fstrand != $_->strand;
	    if( defined $_->seq_id ) {
		$mixedloc = 1 if( $_->seq_id ne $seqid );
	    }
	    [ $_, $_->start * ($_->strand || 1)];
	} @locset;

	if ( $mixed ) {
	    $self->warn("Mixed strand locations, spliced seq using the input order rather than trying to sort");
	    @locs = @locset;
	}
    } else {
	# use the original order instead of trying to sort
	@locs = @locset;
	$fstrand = $locs[0]->strand;
    }

    foreach my $loc ( @locs ) {
	if( ! $loc->isa("Bio::Location::Atomic") ) {
	    $self->throw("Can only deal with one level deep locations");
	}
	my $called_seq;
	if( $fstrand != $loc->strand ) {
	    $self->warn("feature strand is different from location strand!");
	}
	# deal with remote sequences

	if( defined $loc->seq_id &&
	    $loc->seq_id ne $seqid ) {
	    if( defined $db ) {
		my $sid = $loc->seq_id;
		$sid =~ s/\.\d+$//g;
		eval {
		    $called_seq = $db->get_Seq_by_acc($sid);
		};
		if( $@ ) {
		    $self->warn("In attempting to join a remote location, sequence $sid was not in database. Will provide padding N's. Full exception\n\n $@");
		    $called_seq = undef;
		}
	    } else {
		$self->warn( "cannot get remote location for ".$loc->seq_id ." without a valid Bio::DB::RandomAccessI database handle (like Bio::DB::GenBank)");
		$called_seq = undef;
	    }
	    if( !defined $called_seq ) {
		$seqstr .= 'N' x $self->length;
		next;
	    }
	} else {
	    $called_seq = $self->entire_seq;
	}

    # does the called sequence make sense? Bug 1780
    if ($called_seq->length < $loc->end) {
        my $accession = $called_seq->accession;
        my $end = $loc->end;
        my $length = $called_seq->length;
        my $orig_id = $self->seq_id; # originating sequence
        my ($locus) = $self->get_tagset_values("locus_tag");
        $self->throw("Location end ($end) exceeds length ($length) of ".
                     "called sequence $accession.\nCheck sequence version used in ".
                     "$locus locus-tagged SeqFeature in $orig_id.");
    }

	if( $self->isa('Bio::Das::SegmentI') ) {
	    my ($s,$e) = ($loc->start,$loc->end);
	    $seqstr .= $called_seq->subseq($s,$e)->seq();
	} else {
	    # This is dumb, subseq should work on locations...
	    if( $loc->strand == 1 ) {
		$seqstr .= $called_seq->subseq($loc->start,$loc->end);
	    } else {
		if( $nosort ) {
		    $seqstr = $called_seq->trunc($loc->start,$loc->end)->revcom->seq() . $seqstr;
		} else {
		    $seqstr .= $called_seq->trunc($loc->start,$loc->end)->revcom->seq();
		}
	    }
	}
    }
    my $out = Bio::Seq->new( -id => $self->entire_seq->display_id
			            . "_spliced_feat",
			     -seq => $seqstr);

    return $out;
}
locationdescriptionprevnextTop
sub location {
   my ($self) = @_;

   $self->throw_not_implemented();
}
primary_iddescriptionprevnextTop
sub primary_id {
    my $self = shift;
    # note from cjm@fruitfly.org:
    # I have commented out the following 2 lines:

    #return $self->{'primary_id'} = shift if @_;
    #return $self->{'primary_id'};

    #... and replaced it with the following; see
    # http://bioperl.org/pipermail/bioperl-l/2003-December/014150.html
    # for the discussion that lead to this change

    if (@_) {
        if ($self->has_tag('ID')) {
            $self->remove_tag('ID');
        }
        $self->add_tag_value('ID', shift);
    }
    my ($id) = $self->get_tagset_values('ID');
    return $id;
}
generate_unique_persistent_iddescriptionprevnextTop
sub generate_unique_persistent_id {
    # DEPRECATED - us IDHandler
    my $self = shift;
    require "Bio/SeqFeature/Tools/IDHandler.pm";
    Bio::SeqFeature::Tools::IDHandler->new->generate_unique_persistent_id($self);
}
General documentation
FEEDBACKTop
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
Reporting BugsTop
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/
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
Bio::SeqFeatureI specific methodsTop
New method interfaces.
Decorating methodsTop
These methods have an implementation provided by Bio::SeqFeatureI,
but can be validly overwritten by subclasses
Bio::RangeI methodsTop
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()Top
 See Bio::RangeI
end()Top
 See Bio::RangeI
strand()Top
 See Bio::RangeI
overlaps()Top
 See Bio::RangeI
contains()Top
 See Bio::RangeI
equals()Top
 See Bio::RangeI
intersection()Top
 See Bio::RangeI
union()Top
 See Bio::RangeI
Bio::AnnotatableI methodsTop
has_tag()Top
 Deprecated.  See Bio::AnnotatableI
remove_tag()Top
 Deprecated.  See Bio::AnnotatableI
add_tag_value()Top
 Deprecated.  See Bio::AnnotatableI
get_tag_values()Top
 Deprecated.  See Bio::AnnotatableI
get_tagset_values()Top
 Deprecated.  See Bio::AnnotatableI
get_all_tags()Top
 Deprecated.  See Bio::AnnotatableI