Bio::LiveSeq::Mutation.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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 lenght 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