NAME

FAST::Bio::SeqFeature::Generic - Generic SeqFeature

SYNOPSIS

$feat = FAST::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 = FAST::Bio::SeqFeature::Generic->new( -gff_string => $string );
# if you want explicitly GFF1
$feat = FAST::Bio::SeqFeature::Generic->new( -gff1_string => $string );

# add it to an annotated sequence

$annseq->add_SeqFeature($feat);

DESCRIPTION

FAST::Bio::SeqFeature::Generic is a generic implementation for the FAST::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 FAST::Bio::SeqFeature::Gene, FAST::Bio::SeqFeature::Transcript and FAST::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 FAST::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 FAST::Bio::SeqIO system

Implemented Interfaces

This class implementes the following interfaces.

FAST::Bio::SeqFeatureI

Note that this includes implementing FAST::Bio::RangeI.

FAST::Bio::AnnotatableI

FAST::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://redmine.open-bio.org/projects/bioperl/

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         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 $obj = FAST::Bio::SeqFeature::Generic->direct_new
Function: create a blessed hash - for performance improvement in 
          object creation
Returns : FAST::Bio::SeqFeature::Generic object
Args    : none

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 : FAST::Bio::LocationI object
Args    : [optional] FAST::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    : none

end

Title   : end
Usage   : $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 = $feature->length
Function: Get the feature length computed as 
          $feat->end - $feat->start + 1
Returns : integer
Args    : none

strand

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    : none

score

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 set

frame

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 set

primary_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    : none

source_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    : none

has_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 tag

add_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 tag

get_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 FAST::Bio::Seq object to this feature. This
          FAST::Bio::Seq object is for the *entire* sequence: ie
          from 1 to 10000
Example :
Returns : TRUE on success
Args    : a FAST::Bio::PrimarySeqI compliant object

seq

Title   : seq
Usage   : $tseq = $sf->seq()
Function: returns the truncated sequence (if there) for this
Example :
Returns : sub seq (a FAST::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 FAST::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 FAST::Bio::AnnotatableI

annotation

Title   : annotation
Usage   : $obj->annotation($annot_obj)
Function: Get/set the annotation collection object for annotating this
          feature.

Example : 
Returns : A FAST::Bio::AnnotationCollectionI object
Args    : newvalue (optional)

Methods to implement FAST::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    : 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
Returns : nothing
Args    : An object which has the SeqFeatureI interface

remove_SeqFeatures

Title   : remove_SeqFeatures
Usage   : $sf->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 FAST::Bio::SeqFeatureI implementing features that was
          deleted.
Args    : none

GFF-related methods

gff_format

Title   : gff_format
Usage   : # get:
          $gffio = $feature->gff_format();
          # set (change the default version of GFF2):
          $feature->gff_format(FAST::Bio::Tools::GFF->new(-gff_version => 1));
Function: Get/set the GFF format interpreter. This object is supposed to 
          format and parse GFF. See FAST::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 FAST::Bio::Tools::GFF compliant object
Args    : On set, an instance of FAST::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 FAST::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   : @features = FAST::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 FAST::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   : $self->_expand_region($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_sub_SeqFeature() already does this.
Returns : 
Args    : A FAST::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.

cpanm FAST

perl -MCPAN -e shell
install FAST