NAME
Bio::SeqFeature::Generic - Generic SeqFeature
SYNOPSIS
$feat = new Bio::SeqFeature::Generic ( -start => 10, -end => 100,
-strand => -1, -primary => 'repeat',
-source_tag => 'repeatmasker',
-display_name => 'alu family',
-score => 1000,
-tag => {
new => 1,
author => 'someone',
sillytag => 'this is silly!' } );
$feat = new Bio::SeqFeature::Generic ( -gff_string => $string );
# if you want explicitly GFF1
$feat = new Bio::SeqFeature::Generic ( -gff1_string => $string );
# add it to an annotated sequence
$annseq->add_SeqFeature($feat);DESCRIPTION
Bio::SeqFeature::Generic is a generic implementation for the Bio::SeqFeatureI interface, providing a simple object to provide all the information for a feature on a sequence.
For many Features, this is all you will need to use (for example, this is fine for Repeats in DNA sequence or Domains in protein sequence). For other features, which have more structure, this is a good base class to extend using inheritence to have new things: this is what is done in the Bio::SeqFeature::Gene, Bio::SeqFeature::Transcript and Bio::SeqFeature::Exon, which provide well coordinated classes to represent genes on DNA sequence (for example, you can get the protein sequence out from a transcript class).
For many Features, you want to add some piece of information, for example a common one is that this feature is 'new' whereas other features are 'old'. The tag system, which here is implemented using a hash can be used here. You can use the tag system to extend the SeqFeature::Generic programmatically: that is, you know that you have read in more information into the tag 'mytag' which you can then retrieve. This means you do not need to know how to write inherieted Perl to provide more complex information on a feature, and/or, if you do know but you do not want to write a new class every time you need some extra piece of information, you can use the tag system to easily store and then retrieve information.
The tag system can be written in/out of GFF format, and also into EMBL format via the SeqIO system
Implemented Interfaces
This class implementes the following interfaces.
- Bio::SeqFeatureI
-
Note that this includes implementing Bio::RangeI.
- Bio::AnnotatableI
- Bio::FeatureHolderI
-
Features held by a feature are essentially sub-features.
FEEDBACK
Mailing Lists
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 listsReporting 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 email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/AUTHOR - Ewan Birney
Ewan Birney <birney@sanger.ac.uk>
DEVELOPERS
This class has been written with an eye out of inheritence. The fields the actual object hash are:
_gsf_tag_hash = reference to a hash for the tags
_gsf_sub_array = reference to an array for subfeaturesAPPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
set_attributes
Title : set_attributes
Usage :
Function: Sets a whole array of parameters at once.
Example :
Returns : none
Args : Named parameters, in the form as they would otherwise be passed
to new(). Currently recognized are:
-start start position
-end end position
-strand strand
-primary primary tag
-source source tag
-frame frame
-score score value
-tag a reference to a tag/value hash
-gff_string GFF v.2 string to initialize from
-gff1_string GFF v.1 string to initialize from
-seq_id the display name of the sequence
-annotation the AnnotationCollectionI object
-location the LocationI objectdirect_new
Title : direct_new
Usage : my $obj = Bio::SeqFeature::Generic->direct_new
Function: create a blessed hash - for performance improvement in
object creation
Returns : Bio::SeqFeature::Generic object
Args : nonelocation
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 : [optional] Bio::LocationI object to set the value to.start
Title : start
Usage : $start = $feat->start
$feat->start(20)
Function: Get/set on the start coordinate of the feature
Returns : integer
Args : noneend
Title : end
Usage : $end = $feat->end
$feat->end($end)
Function: get/set on the end coordinate of the feature
Returns : integer
Args : nonelength
Title : length
Usage : my $len = $feature->length
Function: Get the feature length computed as
$feat->end - $feat->start + 1
Returns : integer
Args : nonestrand
Title : strand
Usage : $strand = $feat->strand()
$feat->strand($strand)
Function: get/set on strand information, being 1,-1 or 0
Returns : -1,1 or 0
Args : nonescore
Title : score
Usage : $score = $feat->score()
$feat->score($score)
Function: get/set on score information
Returns : float
Args : none if get, the new value if setframe
Title : frame
Usage : $frame = $feat->frame()
$feat->frame($frame)
Function: get/set on frame information
Returns : 0,1,2, '.'
Args : none if get, the new value if setprimary_tag
Title : primary_tag
Usage : $tag = $feat->primary_tag()
$feat->primary_tag('exon')
Function: get/set on the primary tag for a feature,
eg 'exon'
Returns : a string
Args : nonesource_tag
Title : source_tag
Usage : $tag = $feat->source_tag()
$feat->source_tag('genscan');
Function: Returns the source tag for a feature,
eg, 'genscan'
Returns : a string
Args : nonehas_tag
Title : has_tag
Usage : $value = $self->has_tag('some_tag')
Function: Tests wether a feature contaings a tag
Returns : TRUE if the SeqFeature has the tag,
and FALSE otherwise.
Args : The name of a tagadd_tag_value
Title : add_tag_value
Usage : $self->add_tag_value('note',"this is a note");
Returns : TRUE on success
Args : tag (string) and one or more values (any scalar(s))get_tag_values
Title : get_tag_values
Usage : @values = $gsf->get_tag_values('note');
Function: Returns a list of all the values stored
under a particular tag.
Returns : A list of scalars
Args : The name of the tagget_all_tags
Title : get_all_tags
Usage : @tags = $feat->get_all_tags()
Function: Get a list of all the tags in a feature
Returns : An array of tag names
Args : none# added a sort so that tags will be returned in a predictable order # I still think we should be able to specify a sort function # to the object at some point # -js
remove_tag
Title : remove_tag
Usage : $feat->remove_tag('some_tag')
Function: removes a tag from this feature
Returns : the array of values for this tag before removing it
Args : tag (string)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
Example :
Returns : TRUE on success
Args : a Bio::PrimarySeqI compliant objectseq
Title : seq
Usage : $tseq = $sf->seq()
Function: returns the truncated sequence (if there) for this
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 : noneentire_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 :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)display_name
Title : display_name
Usage : $featname = $obj->display_name
Function: Implements the display_name() method, which is a human-readable
name for the feature.
Returns : value of display_name (a string)
Args : Optionally, on set the new value or undef Methods for implementing Bio::AnnotatableI
annotation
Title : annotation
Usage : $obj->annotation($annot_obj)
Function: Get/set the annotation collection object for annotating this
feature.
Example :
Returns : A Bio::AnnotationCollectionI object
Args : newvalue (optional)Methods to implement Bio::FeatureHolderI
This includes methods for retrieving, adding, and removing features. Since this is already a feature, features held by this feature holder are essentially sub-features.
get_SeqFeatures
Title : get_SeqFeatures
Usage : @feats = $feat->get_SeqFeatures();
Function: Returns an array of sub Sequence Features
Returns : An array
Args : noneadd_SeqFeature
Title : add_SeqFeature
Usage : $feat->add_SeqFeature($subfeat);
$feat->add_SeqFeature($subfeat,'EXPAND')
Function: adds a SeqFeature into the subSeqFeature array.
with no 'EXPAND' qualifer, subfeat will be tested
as to whether it lies inside the parent, and throw
an exception if not.
If EXPAND is used, the parent's start/end/strand will
be adjusted so that it grows to accommodate the new
subFeature
Returns : nothing
Args : An object which has the SeqFeatureI interfaceremove_SeqFeatures
Title : remove_SeqFeatures
Usage : $sf->remove_SeqFeatures
Function: Removes all sub SeqFeatures
If you want to remove only a subset, remove that subset from the
returned array, and add back the rest.
Example :
Returns : The array of Bio::SeqFeatureI implementing sub-features that was
deleted from this feature.
Args : noneGFF-related methods
gff_format
Title : gff_format
Usage : # get:
$gffio = $feature->gff_format();
# set (change the default version of GFF2):
$feature->gff_format(Bio::Tools::GFF->new(-gff_version => 1));
Function: Get/set the GFF format interpreter. This object is supposed to
format and parse GFF. See Bio::Tools::GFF for the interface.
If this method is called as class method, the default for all
newly created instances will be changed. Otherwise only this
instance will be affected.
Example :
Returns : a Bio::Tools::GFF compliant object
Args : On set, an instance of Bio::Tools::GFF or a derived object.gff_string
Title : gff_string
Usage : $str = $feat->gff_string;
$str = $feat->gff_string($gff_formatter);
Function: Provides the feature information in GFF format.
We override this here from Bio::SeqFeatureI in order to use the
formatter returned by gff_format().
Returns : A string
Args : Optionally, an object implementing gff_string()._from_gff_string
Title : _from_gff_string
Usage :
Function: Set feature properties from GFF string.
This method uses the object returned by gff_format() for the
actual interpretation of the string. Set a different GFF format
interpreter first if you need a specific version, like GFF1. (The
default is GFF2.)
Example :
Returns :
Args : a GFF-formatted string_expand_region
Title : _expand_region
Usage : $self->_expand_region($feature);
Function: Expand the total region covered by this feature to
accomodate for the given feature.
May be called whenever any kind of subfeature is added to this
feature. add_sub_SeqFeature() already does this.
Returns :
Args : A Bio::SeqFeatureI implementing object._parse
Title : _parse
Usage :
Function: Parsing hints
Example :
Returns :
Args :_tag_value
Title : _tag_value
Usage :
Function: For internal use only. Convenience method for those tags that
may only have a single value.
Returns : The first value under the given tag as a scalar (string)
Args : The tag as a string. Optionally, the value on set.