Christopher Fields > BioPerl > Bio::SeqFeature::Gene::Exon



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Module Version: 1.006924   Source  


Bio::SeqFeature::Gene::Exon - a feature representing an exon


    # obtain an exon instance $exon somehow
    print "exon from ", $exon->start(), " to ", $exon->end(),
          " on seq ", $exon->seq_id(), ", strand ", $exon->strand(),
          ", encodes the peptide sequence ", 
          $exon->cds()->translate()->seq(), "\n";


This module implements a feature representing an exon by implementing the Bio::SeqFeature::Gene::ExonI interface. By default an Exon is coding. Supply -is_coding => 0 to the constructor or call $exon->is_coding(0) otherwise.

Apart from that, this class also implements Bio::SeqFeatureI by inheriting off Bio::SeqFeature::Generic.


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AUTHOR - Hilmar Lapp ^



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


 Title   : is_coding
 Usage   : if($exon->is_coding()) {
                   # do something
           if($is_utr) {
 Function: Get/set whether or not the exon codes for amino acid.
 Returns : TRUE if the object represents a feature translated into protein,
           and FALSE otherwise.
 Args    : A boolean value on set.


 Title   : primary_tag
 Usage   : $tag = $feat->primary_tag()
 Function: Get/set the primary tag for the exon feature.

           This method is overridden here in order to allow only for
           tag values following a certain convention. For consistency reasons,
           the tag value must either contain the string 'exon' or the string
           'utr' (both case-insensitive). In the case of 'exon', a string
           describing the type of exon may be appended or prefixed. Presently,
           the following types are allowed: initial, internal, and terminal
           (all case-insensitive). 

           If the supplied tag value matches 'utr' (case-insensitive),
           is_coding() will automatically be set to FALSE, and to TRUE

 Returns : A string.
 Args    : A string on set.


 Title   : location
 Usage   : my $location = $exon->location()
 Function: Returns a location object suitable for identifying the location 
           of the exon on the sequence or parent feature.

           This method is overridden here to restrict allowed location types
           to non-compound locations.

 Returns : Bio::LocationI object
 Args    : none


 Title   : cds()
 Usage   : $cds = $exon->cds();
 Function: Get the coding sequence of the exon as a sequence object.

           The sequence of the returned object is prefixed by Ns (lower case)
           if the frame of the exon is defined and different from zero. The
           result is that the first base starts a codon (frame 0).

           This implementation returns undef if the particular exon is
           not translated to protein, i.e., is_coding() returns FALSE. Undef
           will also be returned if no sequence is attached to this exon

 Returns : A Bio::PrimarySeqI implementing object.
 Args    : 
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