bio::seqfeature::gene::exoni(3pm) [debian man page]

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

NAME

       Bio::SeqFeature::Gene::ExonI - Interface for a feature representing an exon

SYNOPSIS

       See documentation of methods.

DESCRIPTION

       A feature representing an exon. An exon in this definition is transcribed and at least for one particular transcript not spliced out of the
       pre-mRNA. However, it does not necessarily code for amino acid.

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
		  }
	Function: Whether or not the exon codes for amino acid.
	Returns : TRUE if the object represents a feature translated into protein,
		  and FALSE otherwise.
	Args	:

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

		  The returned sequence object must be in frame 0, i.e., the first
		  base starts a codon.

		  An implementation may return undef, indicating that a coding
		  sequence does not exist, e.g. for a UTR (untranslated region).

	Returns : A L<Bio::PrimarySeqI> implementing object.
	Args	:

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

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

NAME

       Bio::SeqFeature::Gene::GeneStructure - A feature representing an arbitrarily complex structure of a gene

SYNOPSIS

	 # See documentation of methods.

DESCRIPTION

       A feature representing a gene structure. As of now, a gene structure really is only a collection of transcripts. See
       Bio::SeqFeature::Gene::TranscriptI (interface) and Bio::SeqFeature::Gene::Transcript (implementation) for the features of such objects.

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-at-gmx.net

APPENDIX

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

   transcripts
	Title	: transcripts
	Usage	: @transcripts = $gene->transcripts();
	Function: Get the transcripts of this gene structure. Many gene structures
		  will have only one transcript.

	Returns : An array of Bio::SeqFeature::Gene::TranscriptI implementing objects.
	Args	:

   add_transcript
	Title	: add_transcript()
	Usage	: $gene->add_transcript($transcript);
	Function: Add a transcript to this gene structure.
	Returns :
	Args	: A Bio::SeqFeature::Gene::TranscriptI implementing object.

   flush_transcripts
	Title	: flush_transcripts()
	Usage	: $gene->flush_transcripts();
	Function: Remove all transcripts from this gene structure.
	Returns :
	Args	:

   add_transcript_as_features
	Title	: add_transcript_as_features
	Usage	: $gene->add_transcript_as_features(@featurelist);
	Function: take a list of Bio::SeqFeatureI objects and turn them into a
		  Bio::SeqFeature::Gene::Transcript object.  Add that transcript to the gene.
	Returns : nothing
	Args	: a list of Bio::SeqFeatureI compliant objects

   promoters
	Title	: promoters
	Usage	: @prom_sites = $gene->promoters();
	Function: Get the promoter features of this gene structure.

		  This method basically merges the promoters returned by transcripts.

		  Note that OO-modeling of regulatory elements is not stable yet.
		  This means that this method might change or even disappear in a
		  future release. Be aware of this if you use it.

	Returns : An array of Bio::SeqFeatureI implementing objects.
	Args	:

   exons
	Title	: exons()
	Usage	: @exons = $gene->exons();
		  @inital_exons = $gene->exons('Initial');
	Function: Get all exon features or all exons of a specified type of this gene
		  structure.

		  Exon type is treated as a case-insensitive regular expression and
		  optional. For consistency, use only the following types:
		  initial, internal, terminal, utr, utr5prime, and utr3prime.
		  A special and virtual type is 'coding', which refers to all types
		  except utr.

		  This method basically merges the exons returned by transcripts.

	Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects.
	Args	: An optional string specifying the type of exon.

   introns
	Title	: introns()
	Usage	: @introns = $gene->introns();
	Function: Get all introns of this gene structure.

		  Note that this class currently generates these features on-the-fly,
		  that is, it simply treats all regions between exons as introns.
		  It assumes that the exons in the transcripts do not overlap.

		  This method basically merges the introns returned by transcripts.

	Returns : An array of Bio::SeqFeatureI implementing objects.
	Args	:

   poly_A_sites
	Title	: poly_A_sites()
	Usage	: @polyAsites = $gene->poly_A_sites();
	Function: Get the poly-adenylation sites of this gene structure.

		  This method basically merges the poly-adenylation sites returned by
		  transcripts.

	Returns : An array of Bio::SeqFeatureI implementing objects.
	Args	:

   utrs
	Title	: utrs()
	Usage	: @utr_sites = $gene->utrs('3prime');
		  @utr_sites = $gene->utrs('5prime');
		  @utr_sites = $gene->utrs();
	Function: Get the features representing untranslated regions (UTR) of this
		  gene structure.

		  You may provide an argument specifying the type of UTR. Currently
		  the following types are recognized: 5prime 3prime for UTR on the
		  5' and 3' end of the CDS, respectively.

		  This method basically merges the UTRs returned by transcripts.

	Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
		  representing the UTR regions or sites.
	Args	: Optionally, either 3prime, or 5prime for the the type of UTR
		  feature.

   sub_SeqFeature
	Title	: sub_SeqFeature
	Usage	: @feats = $gene->sub_SeqFeature();
	Function: Returns an array of all subfeatures.

		  This method is defined in Bio::SeqFeatureI. We override this here
		  to include the transcripts.

	Returns : An array Bio::SeqFeatureI implementing objects.
	Args	: none

   flush_sub_SeqFeature
	Title	: flush_sub_SeqFeature
	Usage	: $gene->flush_sub_SeqFeature();
		  $gene->flush_sub_SeqFeature(1);
	Function: Removes all subfeatures.

		  This method is overridden from Bio::SeqFeature::Generic to flush
		  all additional subfeatures, i.e., transcripts, which is
		  almost certainly not what you want. To remove only features added
		  through $gene->add_sub_SeqFeature($feature) pass any
		  argument evaluating to TRUE.

	Example :
	Returns : none
	Args	: Optionally, an argument evaluating to TRUE will suppress flushing
		  of all gene structure-specific subfeatures (transcripts).

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