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

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NAME ^

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

SYNOPSIS ^

    # 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";

DESCRIPTION ^

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.

FEEDBACK ^

Mailing Lists

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://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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 the web:

  https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Hilmar Lapp ^

Email hlapp@gmx.net

APPENDIX ^

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

is_coding

 Title   : is_coding
 Usage   : if($exon->is_coding()) {
                   # do something
           }
           if($is_utr) {
               $exon->is_coding(0);
           }
 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.

primary_tag

 Title   : primary_tag
 Usage   : $tag = $feat->primary_tag()
           $feat->primary_tag('exon')
 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
           otherwise.

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

location

 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

cds

 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
           feature.

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