bio::updateableseqi(3pm) [debian man page]

Bio::UpdateableSeqI(3pm)				User Contributed Perl Documentation				  Bio::UpdateableSeqI(3pm)

NAME

       Bio::UpdateableSeqI - Descendant of Bio::SeqI that allows updates

SYNOPSIS

       See Bio::SeqI for most of the documentation.  See the documentation of the methods for further details.

DESCRIPTION

       Bio::UpdateableSeqI is an interface for Sequence objects which are expected to allow users to perform basic editing functions
       (update/delete) on their component SeqFeatures.

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 the
       Bioperl mailing list.  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 of the bugs and their resolution. Bug reports can be submitted via the
       web:

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

AUTHOR - David Block
       Email dblock@gene.pbi.nrc.ca

CONTRIBUTORS

       Ewan Birney forced me to this...

APPENDIX

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

   delete_feature
	Title	: delete_feature
	Usage	: my $orphanlist=$self->delete_feature($feature,$transcript,$gene);
	Function: deletes the specified $feature from the given transcript, if $transcript is sent and exists and $feature is a feature of $transcript,
		  or from $gene if the $feature is a feature of $gene, or from $self if $transcript and $gene are not sent.  Keeps track of the features
		  of the $gene object that may be left as orphans and returns them as a listref.
	Example : I want to delete transcript 'abc' of gene 'def', with three exons, leaving only transcript 'ghi' with two exons.
		  This will leave exons 1 and 3 part of 'ghi', but exon 2 will become an orphan.
		  my $orphanlist=$seq->delete_feature($transcript{'abc'},undef,$gene{'def'});
		  $orphanlist is a reference to a list containing $exon{'2'};
	Returns : a listref of orphaned features after the deletion of $feature (optional)
	Args	: $feature - the feature to be deleted
		  $transcript - the transcript containing the $feature, so that a $feature can be removed from only one transcript when there are multiple
				transcripts in a gene.
		  $gene - the gene containing the $transcript and/or the $feature

perl v5.14.2							    2012-03-02						  Bio::UpdateableSeqI(3pm)

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

NAME

       Bio::SeqFeature::Gene::TranscriptI - Interface for a feature representing a
		transcript of exons, promoter(s), UTR, and a poly-adenylation site.

SYNOPSIS

	 #documentation needed

DESCRIPTION

       A feature representing a transcript.

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 _

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

		  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 representing the
		  promoter regions or sites.
	Args	:

   exons
	Title	: exons()
	Usage	: @exons = $transcript->exons();
		  @inital = $transcript->exons('Initial');
	Function: Get the individual exons this transcript comprises of, or all exons
		  of a specified type.

		  Refer to the documentation of the class that produced this
		  transcript object for information about the possible types.

		  See Bio::SeqFeature::Gene::ExonI for properties of the
		  returned objects.

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

   introns
	Title	: introns()
	Usage	: @introns = $transcript->introns();
	Function: Get all introns this transcript comprises of.
	Returns : An array of Bio::SeqFeatureI implementing objects representing the
		  introns.
	Args	:

   poly_A_site
	Title	: poly_A_site()
	Usage	: $polyAsite = $transcript->poly_A_site();
	Function: Get the poly-adenylation site of this transcript.
	Returns : A Bio::SeqFeatureI implementing object.
	Args	:

   utrs
	Title	: utrs()
	Usage	: @utr_sites = $transcript->utrs();
	Function: Get the UTR regions this transcript comprises of.

		  See Bio::SeqFeature::Gene::ExonI for properties of the
		  returned objects.

	Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
	Args	:

   mrna
	Title	: mrna()
	Usage	: $mrna = $transcript->mrna();
	Function: Get the mRNA of the transcript as a sequence object.

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

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

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

   protein
	Title	: protein()
	Usage	: $protein = $transcript->protein();
	Function: Get the protein encoded by the transcript as a sequence object.

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

   parent
	Title	: parent
	Usage	: $obj->parent($newval)
	Function: get the parent gene of the transcript
	Returns : value of parent - a Bio::SeqFeature::Gene::GeneStructureI-compliant object
	Args	: a Bio::SeqFeature::Gene::GeneStructureI-compliant object (optional)

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