Bio
SeqFeatureI
Summary
Bio::SeqFeatureI - Abstract interface of a Sequence Feature
Package variables
Privates (from "my" definitions)
$static_gff_formatter = undef
Included modules
Inherit
Synopsis
# get a seqfeature somehow, eg,
foreach $feat ( $annseq->all_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->sub_SeqFeature();
}
Description
This interface is the functions one can expect for any Sequence
Feature, whatever its implemtation 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
Methods description
Title : sub_SeqFeature
Usage : @feats = $feat->sub_SeqFeature();
Function: Returns an array of sub Sequence Features
Returns : An array
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 : each_tag_value
Usage : @values = $self->each_tag_value('some_tag')
Function:
Returns : An array comprising the values of the specified tag.
Args : |
Title : all_tags
Usage : @tags = $feat->all_tags()
Function: gives all tags for this feature
Returns : an array of strings
Args : none |
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 : |
Title : location
Usage : my $location = $seqfeature->location()
Function: returns a location object suitable for identifying location
of feature on sequence or parent feature
Returns : Bio::LocationI object
Args : none |
Methods code
sub sub_SeqFeature
{ my ($self,@args) = @_;
$self->throw_not_implemented(); } | sub primary_tag
{ my ($self,@args) = @_;
$self->throw_not_implemented(); } | sub source_tag
{ my ($self,@args) = @_;
$self->throw_not_implemented(); } | sub has_tag
{ my ($self,@args) = @_;
$self->throw_not_implemented(); } | sub each_tag_value
{ my ($self,@args) = @_;
$self->throw_not_implemented(); } | sub all_tags
{ my ($self,@args) = @_;
$self->throw_not_implemented(); } | sub gff_string
{ my ($self,$formatter) = @_;
$formatter = $self->_static_gff_formatter unless $formatter;
return $formatter->gff_string($self); } | sub _static_gff_formatter
{ my ($self,@args) = @_;
if( !defined $static_gff_formatter ) {
$static_gff_formatter = Bio::Tools::GFF->new('-gff_version' => 2);
}
return $static_gff_formatter;} | sub location
{ my ($self) = @_;
$self->throw_not_implemented(); } | General documentation
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://bio.perl.org/MailList.html - About the mailing lists
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:
bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
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 = $feat->strand()
Function: Returns strand information, being 1,-1 or 0
Returns : -1,1 or 0
Args : none
| SeqFeatureI specific methods | Top |
New method interfaces.
These methods are inherited from RangeI and can be used
directly from a SeqFeatureI interface. Remember that a
SeqFeature is-a RangeI, and so wherever you see RangeI you
can use a feature ($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