Bio SeqFeatureI
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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,
foreach $feat ( $seq->top_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 } foreach $tag ( $feat->all_tags() ) { print "Feature has tag ", $tag, "with values, ", join(' ',$feat->each_tag_value($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 doesn\'t 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 description
_static_gff_formattercode    nextTop
 Title   : _static_gff_formatter
Usage :
Example :
Returns :
Args :
 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   : display_name
Usage : $name = $feat->display_name()
Function: Returns the human-readable name of the feature for displays.
Returns : a string
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   : get_SeqFeatures
Usage : @feats = $feat->get_SeqFeatures();
Function: Returns an array of sub Sequence Features
Returns : An array
Args : none
 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   : get_tag_values
Usage : @values = $self->get_tag_values('some_tag')
Returns : An array comprising the values of the specified tag.
Args :
 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   : has_tag
Usage : $tag_exists = $self->has_tag('some_tag')
Returns : TRUE if the specified tag exists, and FALSE otherwise
Args :
 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_tag
Usage : $tag = $feat->primary_tag()
Function: Returns the primary tag for a feature,
eg 'exon'
Returns : a string
Args : none
 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   : 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   : source_tag
Usage : $tag = $feat->source_tag()
Function: Returns the source tag for a feature,
eg, 'genscan'
Returns : a string
Args : none
  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] A Bio::DB::RandomAccessI compliant object Returns : A Bio::Seq
Methods code
    eval { require Bio::DB::InMemoryCache };
    if( $@ ) { $HasInMemory = 0 }
    else { $HasInMemory = 1
sub _static_gff_formatter {
   my ($self,@args) = @_;

   if( !defined $static_gff_formatter ) {
       $static_gff_formatter = Bio::Tools::GFF->new('-gff_version' => 2);
   return $static_gff_formatter;
sub attach_seq {
sub display_name {
sub entire_seq {
sub get_SeqFeatures {
   my ($self,@args) = @_;

sub get_all_tags {
sub get_tag_values {
sub gff_string {
   my ($self,$formatter) = @_;

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

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

sub location {
   my ($self) = @_;


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

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

sub spliced_seq {
    my $self = shift;
    my $db = shift;

    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( defined $db && ref($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->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 @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)]; } $self->location->each_Location; if ( $mixed ) { $self->warn("Mixed strand locations, spliced seq using the input ". "order rather than trying to sort"); @locs = $self->location->each_Location; } elsif( $mixedloc ) { # we'll use the prescribed location order
@locs = $self->location->each_Location; } 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; } 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 { $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;
General documentation
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of the Bioperl mailing lists. Your participation is much appreciated.                     - General discussion - 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 email
or the web:
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
SeqFeatureI specific methodsTop
New method interfaces.
Bio::RangeI methodsTop
List of interfaces inherited from Bio::RangeI (see Bio::RangeI
for details).
 Title   : start
Usage : $start = $feat->start
Function: Returns the start coordinate of the feature
Returns : integer
Args : none
 Title   : end
Usage : $end = $feat->end
Function: Returns the end coordinate of the feature
Returns : integer
Args : none
 Title   : strand
Usage : $strand = $feat->strand()
Function: Returns strand information, being 1,-1 or 0
Returns : -1,1 or 0
Args : none
Decorating methodsTop
These methods have an implementation provided by Bio::SeqFeatureI,
but can be validly overwritten by subclasses
RangeI methodsTop
These methods are inherited from RangeI and can be used
directly from a SeqFeatureI interface. Remember that a
SeqFeature is-a RangeI, and so wherever you see RangeI you
can use a feature ($r in the below documentation).
  Title   : overlaps
Usage : if($feat->overlaps($r)) { do stuff }
if($feat->overlaps(200)) { do stuff }
Function: tests if $feat overlaps $r
Args : a RangeI to test for overlap with, or a point
Returns : true if the Range overlaps with the feature, false otherwise
  Title   : contains
Usage : if($feat->contains($r) { do stuff }
Function: tests whether $feat totally contains $r
Args : a RangeI to test for being contained
Returns : true if the argument is totaly contained within this range
  Title   : equals
Usage : if($feat->equals($r))
Function: test whether $feat has the same start, end, strand as $r
Args : a RangeI to test for equality
Returns : true if they are describing the same range
Geometrical methodsTop
These methods do things to the geometry of ranges, and return
triplets (start, stop, strand) from which new ranges could be built.
  Title   : intersection
Usage : ($start, $stop, $strand) = $feat->intersection($r)
Function: gives the range that is contained by both ranges
Args : a RangeI to compare this one to
Returns : nothing if they do not overlap, or the range that they do overlap
  Title   : union
Usage : ($start, $stop, $strand) = $feat->union($r);
: ($start, $stop, $strand) = Bio::RangeI->union(@ranges);
Function: finds the minimal range that contains all of the ranges
Args : a range or list of ranges to find the union of
Returns : the range containing all of the ranges