NAME

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

SYNOPSIS

  # full description 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://github.com/bioperl/bioperl-live/issues

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

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq