Bio::SeqFeature::Generic - Generic SeqFeature
$feat = new Bio::SeqFeature::Generic ( -start => 10, -end => 100, -strand => -1, -primary => 'repeat', -source => 'repeatmasker', -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 the 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 donot 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
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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 sub arrays _gsf_start = scalar of the start point _gsf_end = scalar of the end point _gsf_strand = scalar of the strand
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
Title : start Usage : $start = $feat->start $feat->start(20) Function: Get/set on the start coordinate of the feature Returns : integer Args : none
Title : end Usage : $end = $feat->end $feat->end($end) Function: get/set on the end coordinate of the feature Returns : integer Args : none
Title : length Usage : Function: Example : Returns : Args :
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
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
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
Title : sub_SeqFeature Usage : @feats = $feat->sub_SeqFeature(); Function: Returns an array of sub Sequence Features Returns : An array Args : none
Title : add_sub_SeqFeature Usage : $feat->add_sub_SeqFeature($subfeat); $feat->add_sub_SeqFeature($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
Title : flush_sub_SeqFeature Usage : $sf->flush_sub_SeqFeature Function: Removes all sub SeqFeature (if you want to remove only a subset, take an array of them all, flush them, and add back only the guys you want) Example : Returns : none Args : none
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
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
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
Title : add_tag_value Usage : $self->add_tag_value('note',"this is a note"); Returns : TRUE on success Args : tag (string) and value (any scalar)
Title : each_tag_value Usage : @values = $gsf->each_tag_value('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
Title : all_tags Usage : @tags = $feat->all_tags() Function: Get a list of all the tags in a feature Returns : An array of tag names Args : none
Title : remove_tag Usage : $feat->remove_tag('some_tag') Function: removes a tag from this feature Returns : nothing Args : tag (string)
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 :
Title : seq Usage : $tseq = $sf->seq() Function: returns the truncated sequence (if there) for this Example : Returns : sub seq on attached sequence bounded by start & end Args : none
Title : entire_seq Usage : $whole_seq = $sf->entire_seq() Function: gives the entire sequence that this seqfeature is attached to Example : Returns : Args :
Title : seqname Usage : $obj->seqname($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 seqname. 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 seqname Args : newvalue (optional)
Title : annotation Usage : $obj->annotation($annot_obj) Function: Example : Returns : A Bio::Annotation object Args : newvalue (optional)
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.
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().
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
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.
Title : _parse Usage : Function: Parsing hints Example : Returns : Args :
Title : _tag_value Usage : Function: For internal use only. Convenience method for those tags that may only have a single value. Returns : Args :
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.