Bio::SeqFeatureI - Abstract interface of a Sequence Feature
# 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
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
New method interfaces.
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')
Function:
Returns : TRUE if the specified tag exists, and FALSE otherwise
Args :
Title : get_tag_values
Usage : @values = $self->get_tag_values('some_tag')
Function:
Returns : An array comprising the values of the specified tag.
Args :
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 : Function: Example : Returns : Args :
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
These methods have an implementation provided by Bio::SeqFeatureI, but can be validly overwritten by subclasses
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
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 $r Args : a RangeI to test for equality Returns : true if they are describing the same range
These methods do things to the geometry of ranges, and return triplets (start, stop, strand) from which new ranges could be built.
Title : intersection Usage : ($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
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
