Bio::SeqFeature::Generic - Generic SeqFeature $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); 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 This class implementes the following interfaces. Note that this includes implementing Bio::RangeI. Features held by a feature are essentially sub-features.

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 lists

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Ewan Birney <birney@sanger.ac.uk> 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 subfeatures 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 object

direct_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 : 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 : 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 : 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 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 : $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 : 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 :

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

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) 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 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 : none

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.