Provided by: libbio-perl-perl_1.7.2-2_all 
NAME
Bio::SeqFeature::Generic - Generic SeqFeature
SYNOPSIS
$feat = Bio::SeqFeature::Generic->new(
-start => 10,
-end => 100,
-strand => -1,
-primary => 'repeat', # -primary_tag is a synonym
-source_tag => 'repeatmasker',
-display_name => 'alu family',
-score => 1000,
-tag => { new => 1,
author => 'someone',
sillytag => 'this is silly!' } );
$feat = Bio::SeqFeature::Generic->new( -gff_string => $string );
# if you want explicitly GFF1
$feat = Bio::SeqFeature::Generic->new( -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 inheritance 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
Bio::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 inherited 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
Bio::SeqIO system
Implemented Interfaces
This class implements 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://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://github.com/bioperl/bioperl-live/issues
AUTHOR - Ewan Birney
Ewan Birney <birney@sanger.ac.uk>
DEVELOPERS
This class has been written with an eye out for inheritance. 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 subfeatures
APPENDIX
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
-phase the phase of the feature (0..2)
-primary_tag primary tag
-primary (synonym for -primary_tag)
-source_tag source tag
-source (synonym for -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 object
direct_new
Title : direct_new
Usage : my $feat = Bio::SeqFeature::Generic->direct_new;
Function: create a blessed hash - for performance improvement in
object creation
Returns : Bio::SeqFeature::Generic object
Args : none
location
Title : location
Usage : my $location = $feat->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 : my $start = $feat->start;
$feat->start(20);
Function: Get/set on the start coordinate of the feature
Returns : integer
Args : none
end
Title : end
Usage : my $end = $feat->end;
$feat->end($end);
Function: get/set on the end coordinate of the feature
Returns : integer
Args : none
length
Title : length
Usage : my $len = $feat->length;
Function: Get the feature length computed as:
$feat->end - $feat->start + 1
Returns : integer
Args : none
strand
Title : strand
Usage : my $strand = $feat->strand();
$feat->strand($strand);
Function: get/set on strand information, being 1,-1 or 0
Returns : -1,1 or 0
Args : none
score
Title : score
Usage : my $score = $feat->score();
$feat->score($score);
Function: get/set on score information
Returns : float
Args : none if get, the new value if set
frame
Title : frame
Usage : my $frame = $feat->frame();
$feat->frame($frame);
Function: get/set on frame information
Returns : 0,1,2, '.'
Args : none if get, the new value if set
primary_tag
Title : primary_tag
Usage : my $tag = $feat->primary_tag();
$feat->primary_tag('exon');
Function: get/set on the primary tag for a feature,
eg 'exon'
Returns : a string
Args : none
source_tag
Title : source_tag
Usage : my $tag = $feat->source_tag();
$feat->source_tag('genscan');
Function: Returns the source tag for a feature,
eg, 'genscan'
Returns : a string
Args : none
has_tag
Title : has_tag
Usage : my $value = $feat->has_tag('some_tag');
Function: Tests whether a feature containings a tag
Returns : TRUE if the SeqFeature has the tag,
and FALSE otherwise.
Args : The name of a tag
add_tag_value
Title : add_tag_value
Usage : $feat->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 : my @values = $feat->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 tag
get_all_tags
Title : get_all_tags
Usage : my @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 : $feat->attach_seq($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 object
seq
Title : seq
Usage : my $tseq = $feat->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.
If the strand is defined and set to -1, the returned sequence is
the reverse-complement of the region
Args : none
entire_seq
Title : entire_seq
Usage : my $whole_seq = $feat->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 : $feat->seq_id($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 : my $featname = $feat->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 : $feat->annotation($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 : my @feats = $feat->get_SeqFeatures();
Function: Returns an array of sub Sequence Features
Returns : An array
Args : none
add_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
!IMPORTANT! The coordinates of the subfeature should not be relative
to the parent feature it is attached to, but relative to the sequence
the parent feature is located on.
Returns : nothing
Args : An object which has the SeqFeatureI interface
remove_SeqFeatures
Title : remove_SeqFeatures
Usage : $feat->remove_SeqFeatures;
Function: Removes all SeqFeatures
If you want to remove only a subset of features then remove that
subset from the returned array, and add back the rest.
Example :
Returns : The array of Bio::SeqFeatureI implementing features that was
deleted.
Args : none
GFF-related methods
gff_format
Title : gff_format
Usage : # get:
my $gffio = $feat->gff_format();
# set (change the default version of GFF2):
$feat->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 : my $str = $feat->gff_string;
my $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().
slurp_gff_file
Title : slurp_file
Usage : my @features = Bio::SeqFeature::Generic::slurp_gff_file(\*FILE);
Function: Sneaky function to load an entire file as in memory objects.
Beware of big files.
This method is deprecated. Use Bio::Tools::GFF instead, which can
also handle large files.
Example :
Returns :
Args :
_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 : $feat->_expand_region($feature);
Function: Expand the total region covered by this feature to
accommodate for the given feature.
May be called whenever any kind of subfeature is added to this
feature. add_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.