Bio::SeqFeatureI(3pm) User Contributed Perl Documentation Bio::SeqFeatureI(3pm)
NAME
Bio::SeqFeatureI - Abstract interface of a Sequence Feature
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(), "
";
if( $feat->strand == 0 ) {
print "Feature applicable to either strand
";
} else {
print "Feature on strand ", $feat->strand,"
"; # -1,1
}
print "feature location is ",$feat->start, "..",
$feat->end, " on strand ", $feat->strand, "
";
print "easy utility to print locations in GenBank/EMBL way ",
$feat->location->to_FTstring(), "
";
foreach $tag ( $feat->get_all_tags() ) {
print "Feature has tag ", $tag, " with values, ",
join(' ',$feat->get_tag_values($tag)), "
";
}
print "new feature
" 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 implementation, it just provides the definitions of what methods one can call. See
Bio::SeqFeature::Generic for a good standard implementation of this object
FEEDBACK
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
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
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:
https://redmine.open-bio.org/projects/bioperl/
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Bio::SeqFeatureI specific methods
New method interfaces.
get_SeqFeatures
Title : get_SeqFeatures
Usage : @feats = $feat->get_SeqFeatures();
Function: Returns an array of sub Sequence Features
Returns : An array
Args : none
display_name
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_tag
Title : primary_tag
Usage : $tag = $feat->primary_tag()
Function: Returns the primary tag for a feature,
eg 'exon'
Returns : a string
Args : none
source_tag
Title : source_tag
Usage : $tag = $feat->source_tag()
Function: Returns the source tag for a feature,
eg, 'genscan'
Returns : a string
Args : none
has_tag
Title : has_tag
Usage : $tag_exists = $self->has_tag('some_tag')
Function:
Returns : TRUE if the specified tag exists, and FALSE otherwise
Args :
get_tag_values
Title : get_tag_values
Usage : @values = $self->get_tag_values('some_tag')
Function:
Returns : An array comprising the values of the specified tag.
Args : a string
throws an exception if there is no such tag
get_tagset_values
Title : get_tagset_values
Usage : @values = $self->get_tagset_values(qw(label transcript_id product))
Function:
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
get_all_tags
Title : get_all_tags
Usage : @tags = $feat->get_all_tags()
Function: gives all tags for this feature
Returns : an array of strings
Args : none
attach_seq
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
seq
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_seq
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_id
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_string
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_formatter
Title : _static_gff_formatter
Usage :
Function:
Example :
Returns :
Args :
Decorating methods
These methods have an implementation provided by Bio::SeqFeatureI, but can be validly overwritten by subclasses
spliced_seq
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 L<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 L<Bio::PrimarySeqI> object
location
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_id
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'
phase
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 field.
Bio::RangeI methods
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()
See L<Bio::RangeI>
end()
See L<Bio::RangeI>
strand()
See L<Bio::RangeI>
overlaps()
See L<Bio::RangeI>
contains()
See L<Bio::RangeI>
equals()
See L<Bio::RangeI>
intersection()
See L<Bio::RangeI>
union()
See L<Bio::RangeI>
perl v5.14.2 2012-03-02 Bio::SeqFeatureI(3pm)