Bio SeqFeatureI
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Bio::SeqFeatureI - Abstract interface of a Sequence Feature
Package variables
Privates (from "my" definitions)
$static_gff_formatter = undef
Included modules
    # 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
implementation, it just provides the definitions of what methods one can
call. See Bio::SeqFeature::Generic for a good standard implementation
of this object
No description
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
 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 :
  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)
(default = if sequence is_circular(), 1, otherwise 0)
-phase truncates the returned sequence based on the
intron phase (0,1,2).
Returns : A 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'
 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
Methods code
    eval { require Bio::DB::InMemoryCache };
    if( $@ ) { $HasInMemory = 0 }
    else { $HasInMemory = 1
sub get_SeqFeatures {
   my ($self,@args) = @_;

sub display_name {
sub primary_tag {
   my ($self,@args) = @_;

sub source_tag {
   my ($self,@args) = @_;

sub has_tag {
   my ($self,@args) = @_;

sub get_tag_values {
sub get_tagset_values {
    my ($self, @args) = @_;
    my @vals = ();
    foreach my $arg (@args) {
        if ($self->has_tag($arg)) {
            push(@vals, $self->get_tag_values($arg));
    return @vals;
sub get_all_tags {
sub attach_seq {
sub seq {
sub entire_seq {
sub seq_id {
sub gff_string {
   my ($self,$formatter) = @_;

   $formatter = $self->_static_gff_formatter unless $formatter;
   return $formatter->gff_string($self);

my $static_gff_formatter = undef;
sub _static_gff_formatter {
   my ($self,@args) = @_;
   require Bio::Tools::GFF; # on the fly inclusion -- is this better?
if( !defined $static_gff_formatter ) { $static_gff_formatter = Bio::Tools::GFF->new('-gff_version' => 2); } return $static_gff_formatter;
sub spliced_seq {
    my $self = shift;
	my @args = @_;
	my ($db, $nosort, $phase) =
	   $self->_rearrange([qw(DB NOSORT PHASE)], @args);
	# set no_sort based on the parent sequence status
if ($self->entire_seq->is_circular) { $nosort = 1; } # (added 7/7/06 to allow use old API (with warnings)
my $old_api = (!(grep {$_ =~ /(?:nosort|db|phase)/} @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; $phase = shift @args if @args; }; if (defined($phase) && ($phase < 0 || $phase > 2)) { $self->warn("Phase must be 0,1, or 2. Setting phase to 0..."); $phase = 0; } 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 = Bio::DB::InMemoryCache->new(-seqdb => $db); } if( ! $self->location->isa("Bio::Location::SplitLocationI") ) { if ($phase) { $self->debug("Subseq start: ",$phase+1,"\tend: ",$self->end,"\n"); my $seqstr = substr($self->seq->seq, $phase); my $out = Bio::Seq->new( -id => $self->entire_seq->display_id . "_spliced_feat", -seq => $seqstr); return $out; } else { 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); # $called_seq is Bio::DB::GFF::RelSegment, as well as its subseq();
# Bio::DB::GFF::RelSegment::seq() returns a Bio::PrimarySeq, and using seq()
# in turn returns a string. Confused?
$seqstr .= $called_seq->subseq($s,$e)->seq()->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,$loc->end)->revcom->seq(); } } } } if (defined($phase)) { $seqstr = substr($seqstr, $phase); } my $out = Bio::Seq->new( -id => $self->entire_seq->display_id . "_spliced_feat", -seq => $seqstr); return $out;
sub location {
   my ($self) = @_;

sub primary_id {
    my $self = shift;
    # note from
# I have commented out the following 2 lines:
#return $self->{'primary_id'} = shift if @_;
#return $self->{'primary_id'};
#... and replaced it with the following; see
# for the discussion that lead to this change
if (@_) { if ($self->has_tag('ID')) { $self->remove_tag('ID'); } $self->add_tag_value('ID', shift); } my ($id) = $self->get_tagset_values('ID'); return $id;
sub generate_unique_persistent_id {
    # DEPRECATED - us IDHandler
my $self = shift; require Bio::SeqFeature::Tools::IDHandler; Bio::SeqFeature::Tools::IDHandler->new->generate_unique_persistent_id($self);
sub phase {
    my $self = shift;
    if( @_ ) {
        $self->remove_tag('phase') if $self->has_tag('phase');
        my $newphase = shift;
        $self->throw("illegal phase value '$newphase', phase must be either undef, 0, 1, or 2")
            unless !defined $newphase || $newphase == 0 || $newphase == 1 || $newphase == 2;
        $self->add_tag_value('phase', $newphase );
        return $newphase;

    return $self->has_tag('phase') ? ($self->get_tag_values('phase'))[0] : undef;
General documentation
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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 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).
 See Bio::RangeI
 See Bio::RangeI
 See Bio::RangeI
 See Bio::RangeI
 See Bio::RangeI
 See Bio::RangeI
 See Bio::RangeI
 See Bio::RangeI