Bio::LiveSeq::Mutator(3pm)				User Contributed Perl Documentation				Bio::LiveSeq::Mutator(3pm)

NAME

       Bio::LiveSeq::Mutator - Package mutating LiveSequences

SYNOPSIS

	 # $gene is a Bio::LiveSeq::Gene object
	 my $mutate = Bio::LiveSeq::Mutator->new('-gene' => $gene,
						 '-numbering' => "coding"
						  );
	 # $mut is a Bio::LiveSeq::Mutation object
	 $mutate->add_Mutation($mut);
	 # $results is a Bio::Variation::SeqDiff object
	 my $results=$mutate->change_gene();
	 if ($results) {
	     my $out = Bio::Variation::IO->new( '-format' => 'flat');
	     $out->write($results);
	 }

DESCRIPTION

       This class mutates Bio::LiveSeq::Gene objects and returns a Bio::Variation::SeqDiff object. Mutations are described as
       Bio::LiveSeq::Mutation objects. See Bio::LiveSeq::Gene, Bio::Variation::SeqDiff, and Bio::LiveSeq::Mutation for details.

FEEDBACK

       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 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 - Heikki Lehvaslaiho &; Joseph A.L. Insana
	 Email:  heikki-at-bioperl-dot-org
		 insana@ebi.ac.uk, jinsana@gmx.net

APPENDIX

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

   gene
	Title	: gene
	Usage	: $mutobj = $obj->gene;
		: $mutobj = $obj->gene($objref);
	Function:

		  Returns or sets the link-reference to a
		  Bio::LiveSeq::Gene object. If no value has ben set, it
		  will return undef

	Returns : an object reference  or undef
	Args	: a Bio::LiveSeq::Gene

       See Bio::LiveSeq::Gene for more information.

   numbering
	Title	: numbering
	Usage	: $obj->numbering();
	Function:

		   Sets and returns coordinate system used in positioning the
		   mutations. See L<change_gene> for details.

	Example :
	Returns : string
	Args	: string (coding [transcript number] | gene | entry)

   add_Mutation
	Title	: add_Mutation
	Usage	: $self->add_Mutation($ref)
	Function: adds a Bio::LiveSeq::Mutation object
	Example :
	Returns :
	Args	: a Bio::LiveSeq::Mutation

       See Bio::LiveSeq::Mutation for more information.

   each_Mutation
	Title	: each_Mutation
	Usage	: foreach $ref ( $a->each_Mutation )
	Function: gets an array of Bio::LiveSeq::Mutation objects
	Example :
	Returns : array of Mutations
	Args	:

       See Bio::LiveSeq::Mutation for more information.

   mutation
	Title	: mutation
	Usage	: $mutobj = $obj->mutation;
		: $mutobj = $obj->mutation($objref);
	Function:

		  Returns or sets the link-reference to the current mutation
		  object.  If the value is not set, it will return undef.
		  Internal method.

	Returns : an object reference  or undef

   DNA
	Title	: DNA
	Usage	: $mutobj = $obj->DNA;
		: $mutobj = $obj->DNA($objref);
	Function:

		  Returns or sets the reference to the LiveSeq object holding
		  the reference sequence. If there is no link, it will return
		  undef.
		  Internal method.

	Returns : an object reference or undef

   RNA
	Title	: RNA
	Usage	: $mutobj = $obj->RNA;
		: $mutobj = $obj->RNA($objref);
	Function:

		  Returns or sets the reference to the LiveSeq object holding
		  the reference sequence. If the value is not set, it will return
		  undef.
		  Internal method.

	Returns : an object reference  or undef

   dnamut
	Title	: dnamut
	Usage	: $mutobj = $obj->dnamut;
		: $mutobj = $obj->dnamut($objref);
	Function:

		  Returns or sets the reference to the current DNAMutation object.
		  If the value is not set, it will return undef.
		  Internal method.

	Returns : a Bio::Variation::DNAMutation object or undef

       See Bio::Variation::DNAMutation for more information.

   rnachange
	Title	: rnachange
	Usage	: $mutobj = $obj->rnachange;
		: $mutobj = $obj->rnachange($objref);
	Function:

		  Returns or sets the reference to the current RNAChange object.
		  If the value is not set, it will return undef.
		  Internal method.

	Returns : a Bio::Variation::RNAChange object or undef

       See Bio::Variation::RNAChange for more information.

   aachange
	Title	: aachange
	Usage	: $mutobj = $obj->aachange;
		: $mutobj = $obj->aachange($objref);
	Function:

		  Returns or sets the reference to the current AAChange object.
		  If the value is not set, it will return undef.
		  Internal method.

	Returns : a Bio::Variation::AAChange object or undef

       See Bio::Variation::AAChange for more information.

   exons
	Title	: exons
	Usage	: $mutobj = $obj->exons;
		: $mutobj = $obj->exons($objref);
	Function:

		  Returns or sets the reference to a current array of Exons.
		  If the value is not set, it will return undef.
		  Internal method.

	Returns : an array of Bio::LiveSeq::Exon objects or undef

       See Bio::LiveSeq::Exon for more information.

   change_gene_with_alignment
	Title	: change_gene_with_alignment
	Usage	: $results=$mutate->change_gene_with_alignment($aln);

	Function:

		  Returns a Bio::Variation::SeqDiff object containing the
		  results of the changes in the alignment. The alignment has
		  to be pairwise and have one sequence named 'QUERY', the
		  other one is assumed to be a part of the sequence from
		  $gene.

		  This method offers a shortcut to change_gene and
		  automates the creation of Bio::LiveSeq::Mutation objects.
		  Use it with almost identical sequnces, e.g. to locate a SNP.

	Args	: Bio::SimpleAlign object representing a short local alignment
	Returns : Bio::Variation::SeqDiff object or 0 on error

       See Bio::LiveSeq::Mutation, Bio::SimpleAlign, and Bio::Variation::SeqDiff  for more information.

   create_mutation
	Title	: create_mutation
	Usage	:
	Function:

		  Formats sequence differences from two sequences into
		  Bio::LiveSeq::Mutation objects which can be applied to a
		  gene.

		  To keep it generic, sequence arguments need not to be
		  Bio::LocatableSeq. Coordinate change to parent sequence
		  numbering needs to be done by the calling code.

		  Called from change_gene_with_alignment

	Args	: Bio::PrimarySeqI inheriting object for the reference sequence
		  Bio::PrimarySeqI inheriting object for the query sequence
		  integer for the start position of the local sequence difference
		  integer for the length of the sequence difference
	Returns : Bio::LiveSeq::Mutation object

   change_gene
	Title	: change_gene
	Usage	: my $mutate = Bio::LiveSeq::Mutator->new(-gene => $gene,
							  numbering => "coding"
							  );
		  # $mut is Bio::LiveSeq::Mutation object
		  $mutate->add_Mutation($mut);
		  my $results=$mutate->change_gene();

	Function:

		  Returns a Bio::Variation::SeqDiff object containing the
		  results of the changes performed according to the
		  instructions present in Mutation(s).	The -numbering
		  argument decides what molecule is being changed and what
		  numbering scheme being used:

		   -numbering => "entry"

		      determines the DNA level, using the numbering from the
		      beginning of the sequence

		   -numbering => "coding"

		      determines the RNA level, using the numbering from the
		      beginning of the 1st transcript

		      Alternative transcripts can be used by specifying
		      "coding 2" or "coding 3" ...

		   -numbering => "gene"

		      determines the DNA level, using the numbering from the
		      beginning of the 1st transcript and inluding introns.
		      The meaning equals 'coding' if the reference molecule
		      is cDNA.

	Args	: Bio::LiveSeq::Gene object
		  Bio::LiveSeq::Mutation object(s)
		  string specifying a numbering scheme (defaults to 'coding')
	Returns : Bio::Variation::SeqDiff object or 0 on error

   _mutationpos2label
	Title	: _mutationpos2label
	Usage	:
	Function: converts mutation positions into labels
	Example :
	Returns : number of valid mutations
	Args	: LiveSeq sequence object

   _set_DNAMutation
	Title	: _set_DNAMutation
	Usage	:
	Function:

		  Stores DNA level mutation attributes before mutation into
		  Bio::Variation::DNAMutation object.  Links it to SeqDiff
		  object.

	Example :
	Returns : Bio::Variation::DNAMutation object
	Args	: Bio::Variation::SeqDiff object

       See Bio::Variation::DNAMutation and Bio::Variation::SeqDiff.

   _set_effects
	Title	: _set_effects
	Usage	:
	Function:

		  Stores RNA and AA level mutation attributes before mutation
		  into Bio::Variation::RNAChange and
		  Bio::Variation::AAChange objects.  Links them to
		  SeqDiff object.

	Example :
	Returns :
	Args	: Bio::Variation::SeqDiff object
		  Bio::Variation::DNAMutation object

       See Bio::Variation::RNAChange, Bio::Variation::RNAChange, Bio::Variation::SeqDiff, and Bio::Variation::DNAMutation.

   _untranslated
	Title	: _untranslated
	Usage	:
	Function:

		  Stores RNA change attributes before mutation
		  into Bio::Variation::RNAChange object.  Links it to
		  SeqDiff object.

	Example :
	Returns :
	Args	: Bio::Variation::SeqDiff object
		  Bio::Variation::DNAMutation object

       See Bio::Variation::RNAChange, Bio::Variation::SeqDiff and Bio::Variation::DNAMutation for details.

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