NAME

Bio::SeqFeatureI - Abstract interface of a Sequence Feature

SYNOPSIS

    # get a seqfeature somehow, eg,

    foreach $feat ( $annseq->all_seqfeatures() ) {
            print "Feature from ", $feat->start, "to ", $feat->end, " Primary tag  " $feat->primary_tag, 
            " From", $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 value," $feat->has_tag($tag), "\n";
            }
        }

DESCRIPTION

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

CONTACT

Describe contact details here

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

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

sub_SeqFeature

 Title   : sub_SeqFeature
 Usage   : @feats = $feat->sub_SeqFeature();
 Function: Returns an array of sub Sequence Features
 Returns : An array
 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   : $value = $self->has_tag('some_tag')
 Function: Returns the value of the tag (undef if 
           none)
 Returns : 
 Args    :

all_tags

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

gff_string

 Title   : gff_string
 Usage   : $str = $feat->gff_string
 Function: provides the feature information in GFF
           version 2 format.
 Returns : A string
 Args    : None

RangeI methods

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

Geometrical methods

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 don't 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

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq