Bio::SeqFeatureI - Abstract interface of a Sequence Feature # get a seqfeature somehow, eg, from a Sequence with Features attached foreach $feat ( $seq->get_SeqFeatures() ) { print "Feature from ", $feat->start, "to ", $feat->end, " Primary tag ", $feat->primary_tag, ", produced by ", $feat->source_tag(), "\n"; if( $feat->strand == 0 ) { print "Feature applicable to either strand\n"; } else { print "Feature on strand ", $feat->strand,"\n"; # -1,1 } print "feature location is ",$feat->start, "..", $feat->end, " on strand ", $feat->strand, "\n"; print "easy utility to print locations in GenBank/EMBL way ", $feat->location->to_FTstring(), "\n"; foreach $tag ( $feat->get_all_tags() ) { print "Feature has tag ", $tag, " with values, ", join(' ',$feat->get_tag_values($tag)), "\n"; } print "new feature\n" if $feat->has_tag('new'); # features can have sub features my @subfeat = $feat->get_SeqFeatures(); } This interface is the functions one can expect for any Sequence Feature, whatever its implementation or whether it is a more complex type (eg, a Gene). This object does not actually provide any implemention, it just provides the definitions of what methods one can call. See Bio::SeqFeature::Generic for a good standard implementation of this object 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/ The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ New method interfaces.

get_SeqFeatures
Title : get_SeqFeatures Usage : @feats = $feat->get_SeqFeatures(); Function: Returns an array of sub Sequence Features Returns : An array Args : none

display_name
Title : display_name Usage : $name = $feat->display_name() Function: Returns the human-readable name of the feature for displays. Returns : a string Args : none

primary_tag
Title : primary_tag Usage : $tag = $feat->primary_tag() Function: Returns the primary tag for a feature, eg 'exon' Returns : a string Args : none

source_tag
Title : source_tag Usage : $tag = $feat->source_tag() Function: Returns the source tag for a feature, eg, 'genscan' Returns : a string Args : none

has_tag
Title : has_tag Usage : $tag_exists = $self->has_tag('some_tag') Function: Returns : TRUE if the specified tag exists, and FALSE otherwise Args :

get_tag_values
Title : get_tag_values Usage : @values = $self->get_tag_values('some_tag') Function: Returns : An array comprising the values of the specified tag. Args : a string throws an exception if there is no such tag

get_tagset_values
Title : get_tagset_values Usage : @values = $self->get_tagset_values(qw(label transcript_id product)) Function: Returns : An array comprising the values of the specified tags, in order of tags Args : An array of strings does NOT throw an exception if none of the tags are not present this method is useful for getting a human-readable label for a SeqFeatureI; not all tags can be assumed to be present, so a list of possible tags in preferential order is provided

get_all_tags
Title : get_all_tags Usage : @tags = $feat->get_all_tags() Function: gives all tags for this feature Returns : an array of strings Args : none

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 Note that it is not guaranteed that if you obtain a feature from an object in bioperl, it will have a sequence attached. Also, implementors of this interface can choose to provide an empty implementation of this method. I.e., there is also no guarantee that if you do attach a sequence, seq() or entire_seq() will not return undef. The reason that this method is here on the interface is to enable you to call it on every SeqFeatureI compliant object, and that it will be implemented in a useful way and set to a useful value for the great majority of use cases. Implementors who choose to ignore the call are encouraged to specifically state this in their documentation. 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 is a sequence attached) for this feature 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 : none

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)

gff_string
Title : gff_string Usage : $str = $feat->gff_string; $str = $feat->gff_string($gff_formatter); Function: Provides the feature information in GFF format. The implementation provided here returns GFF2 by default. If you want a different version, supply an object implementing a method gff_string() accepting a SeqFeatureI object as argument. E.g., to obtain GFF1 format, do the following: my $gffio = Bio::Tools::GFF->new(-gff_version => 1); $gff1str = $feat->gff_string($gff1io); Returns : A string Args : Optionally, an object implementing gff_string().

_static_gff_formatter
Title : _static_gff_formatter Usage : Function: Example : Returns : Args : List of interfaces inherited from Bio::RangeI (see Bio::RangeI for details).

start
Title : start Usage : $start = $feat->start Function: Returns the start coordinate of the feature Returns : integer Args : none

end
Title : end Usage : $end = $feat->end Function: Returns the end coordinate of the feature Returns : integer Args : none

strand
Title : strand Usage : $strand = $feat->strand() Function: Returns strand information, being 1,-1 or 0 Returns : -1,1 or 0 Args : none These methods have an implementation provided by Bio::SeqFeatureI, but can be validly overwritten by subclasses

spliced_seq
Title : spliced_seq Usage : $seq = $feature->spliced_seq() $seq = $feature_with_remote_locations->spliced_seq($db_for_seqs) Function: Provides a sequence of the feature which is the most semantically "relevant" feature for this sequence. A default implementation is provided which for simple cases returns just the sequence, but for split cases, loops over the split location to return the sequence. In the case of split locations with remote locations, eg join(AB000123:5567-5589,80..1144) in the case when a database object is passed in, it will attempt to retrieve the sequence from the database object, and "Do the right thing", however if no database object is provided, it will generate the correct number of N's (DNA) or X's (protein, though this is unlikely). This function is deliberately "magical" attempting to second guess what a user wants as "the" sequence for this feature Implementing classes are free to override this method with their own magic if they have a better idea what the user wants Args : [optional] A Bio::DB::RandomAccessI compliant object Returns : A Bio::Seq These methods are inherited from RangeI and can be used directly from a SeqFeatureI interface. Remember that a SeqFeature is-a RangeI, and so wherever you see RangeI you can use a feature ($r in the below documentation).

overlaps
Title : overlaps Usage : if($feat->overlaps($r)) { do stuff } if($feat->overlaps(200)) { do stuff } Function: tests if $feat overlaps $r Args : a RangeI to test for overlap with, or a point Returns : true if the Range overlaps with the feature, false otherwise

contains
Title : contains Usage : if($feat->contains($r) { do stuff } Function: tests whether $feat totally contains $r Args : a RangeI to test for being contained Returns : true if the argument is totaly contained within this range

equals
Title : equals Usage : if($feat->equals($r)) Function: test whether $feat has the same start, end, strand as $r Args : a RangeI to test for equality Returns : true if they are describing the same range These methods do things to the geometry of ranges, and return triplets (start, stop, strand) from which new ranges could be built.

intersection
Title : intersection Usage : ($start, $stop, $strand) = $feat->intersection($r) Function: gives the range that is contained by both ranges Args : a RangeI to compare this one to Returns : nothing if they do not overlap, or the range that they do overlap

union
Title : union Usage : ($start, $stop, $strand) = $feat->union($r); : ($start, $stop, $strand) = Bio::RangeI->union(@ranges); Function: finds the minimal range that contains all of the ranges Args : a range or list of ranges to find the union of Returns : the range containing all of the ranges

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 : none

primary_id
Title : primary_id Usage : $obj->primary_id($newval) Function: Example : Returns : value of primary_id (a scalar) Args : on set, new value (a scalar or undef, optional)