Bio::SeqFeatureI - Abstract interface of a Sequence Feature
# get a seqfeature somehow, eg, foreach $feat ( $annseq->all_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 } foreach $tag ( $feat->all_tags() ) { print "Feature has tag ", $tag, "with values, ", join(' ',$feat->each_tag_value($tag)), "\n"; } print "new feature\n" if $feat->has_tag('new'); # features can have sub features my @subfeat = $feat->sub_SeqFeature(); }
This interface is the functions one can expect for any Sequence Feature, whatever its implemtation or whether it is a more complex type (eg, a Gene). This object doesn't 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
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://bio.perl.org/bioperl-bugs/
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : start Usage : $start = $feat->start Function: Returns the start coordinate of the feature Returns : integer Args : none
Title : end Usage : $end = $feat->end Function: Returns the end coordinate of the feature Returns : integer Args : none
Title : strand Usage : $strand = $feat->strand() Function: Returns strand information, being 1,-1 or 0 Returns : -1,1 or 0 Args : none
Title : sub_SeqFeature Usage : @feats = $feat->sub_SeqFeature(); Function: Returns an array of sub Sequence Features Returns : An array Args : none
Title : primary_tag Usage : $tag = $feat->primary_tag() Function: Returns the primary tag for a feature, eg 'exon' Returns : a string Args : none
Title : source_tag Usage : $tag = $feat->source_tag() Function: Returns the source tag for a feature, eg, 'genscan' Returns : a string Args : none
Title : has_tag Usage : $tag_exists = $self->has_tag('some_tag') Function: Returns : TRUE if the specified tag exists, and FALSE otherwise Args :
Title : each_tag_value Usage : @values = $self->each_tag_value('some_tag') Function: Returns : An array comprising the values of the specified tag. Args :
Title : all_tags Usage : @tags = $feat->all_tags() Function: gives all tags for this feature Returns : an array of strings Args : none
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().
Title : _static_gff_formatter Usage : Function: Example : Returns : Args :
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 ($r in the below documentation).
Title : overlaps Usage : if($feat->overlaps($r)) { do stuff } if($feat->overlaps(200)) { do stuff } Function: tests if $feat overlaps $r Args : a RangeI to test for overlap with, or a point Returns : true if the Range overlaps with the feature, false otherwise
Title : contains Usage : if($feat->contains($r) { do stuff } Function: tests whether $feat totally contains $r Args : a RangeI to test for being contained Returns : true if the argument is totaly contained within this range
Title : equals Usage : if($feat->equals($r)) Function: test whether $feat has the same start, end, strand as $r Args : a RangeI to test for equality Returns : true if they are describing the same range
These methods do things to the geometry of ranges, and return triplets (start, stop, strand) from which new ranges could be built.
Title : intersection Usage : ($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
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
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
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.