Bio::SeqFeature::Gene::Exon(3pm)			User Contributed Perl Documentation			  Bio::SeqFeature::Gene::Exon(3pm)

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(), "
";

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	:

perl v5.14.2							    2012-03-02					  Bio::SeqFeature::Gene::Exon(3pm)