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

NAME

       Bio::LiveSeq::Mutation - Mutation event descriptor class

SYNOPSIS

	 # full descrition of a point mutation
	 $mutation1a = Bio::LiveSeq::Mutation->new ( -seq => 'A',
						     -seqori => 'T',
						     -pos  => 100,
						     -len => 1 # optional, defaults to length(seq)
						    );

	 # minimal information for a point mutation
	 $mutation1b = Bio::LiveSeq::Mutation->new ( -seq => 'A',
						     -pos  => 100
						     );
	 # insertion
	 $mutation2 = Bio::LiveSeq::Mutation->new ( -seq => 'ATT',
						    -pos  => 100,
						    -len => 0
						    );
	 # deletion
	 $mutation3 = Bio::LiveSeq::Mutation->new ( -seq => '',  # optional
						    -seqori => 'TTG',  # optional
						    -pos  => 100
						    -len => 3
						    );
	 # complex
	 $mutation4 = Bio::LiveSeq::Mutation->new ( -seq => 'CC',
						    -seqori => 'TTG',  # optional
						    -pos  => 100
						    -len => 3
						    );

DESCRIPTION

       This class describes a local mutation event using minimalistic description.  It is not necessary to know anything about the original
       sequence. You need to give the changed sequence, the position of the mutation in the (unidentified) reference sequence, and the length of
       the affected subsequence in the reference sequence. If the original allele sequence is given, the objects applying the mutation into the
       reference sequence (e.g. Bio::LiveSeq::Mutator) might check for its validity.

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 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
       Email:  heikki-at-bioperl-dot-org

APPENDIX

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

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

		   Sets and returns the mutated sequence. No checking is done
		   to validate the symbols.

	Example :
	Returns : string
	Args	: integer

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

		   Sets and returns the original subsequence in the reference
		   sequence. No checking is done to validate the symbols.
		   Optional value.

	Example :
	Returns : string
	Args	: string

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

		   Sets and returns the position of the first element in the
		   sequence.

	Example :
	Returns : string
	Args	: integer

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

		   Sets and returns the len of the affected original allele
		   sequence.  If value is not set, defaults to the length of
		   the mutated sequence (seq).

	Example :
	Returns : string
	Args	: string

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

		   Sets and returns the label of the affected original allele
		   location. Label is a stable identifier whereas location
		   can be changed by mutations. Label comes from
		   l<Bio::LiveSeq::Gene>.

	Example :
	Returns : string
	Args	: string

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

		   Sets and returns the transcript position of the mutation.
		   Set when associated with a reference sequence. Value
		   depends on reference molecule and the co-ordinate system
		   used.

	Example :
	Returns : string
	Args	: integer

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

		   Sets and returns the position of the mutation in an array
		   of mutations to be issued. Set after the validity of the
		   mutation has been confirmed.

	Example :
	Returns : string
	Args	: integer

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

		   Sets and returns the prelabel of the affected original allele
		   location. Prelabel is a stable identifier whereas location
		   can be changed by mutations. Prelabel comes from
		   l<Bio::LiveSeq::Gene>.

	Example :
	Returns : string
	Args	: string

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

		   Sets and returns the postlabel of the affected original allele
		   location. Postlabel is a stable identifier whereas location
		   can be changed by mutations. Postlabel comes from
		   l<Bio::LiveSeq::Gene>.

	Example :
	Returns : string
	Args	: string

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

		   Sets and returns the lastlabel of the affected original allele
		   location. Lastlabel is a stable identifier whereas location
		   can be changed by mutations. Lastlabel comes from
		   l<Bio::LiveSeq::Gene>.

	Example :
	Returns : string
	Args	: string

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