Bio::Variation::DNAMutation.3pm

Langue: en

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

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Variation::DNAMutation - DNA level mutation class

SYNOPSIS

     $dnamut = Bio::Variation::DNAMutation->new
         ('-start'         => $start,
          '-end'           => $end,
          '-length'        => $len,
          '-upStreamSeq'   => $upflank,
          '-dnStreamSeq'   => $dnflank,
          '-proof'         => $proof,
          '-isMutation'    => 1,
          '-mut_number'    => $mut_number
         );
     $a1 = Bio::Variation::Allele->new;
     $a1->seq('a');
     $dnamut->allele_ori($a1);
     my $a2 = Bio::Variation::Allele->new;
     $a2->seq('t');
     $dnamut->add_Allele($a2);
 
     print "Restriction changes are ", $dnamut->restriction_changes, "\n";
 
     # add it to a SeqDiff container object
     $seqdiff->add_Variant($dnamut);
 
 

DESCRIPTION

The instantiable class Bio::Variation::DNAMutation describes basic sequence changes in genomic DNA level. It uses methods defined in superclass Bio::Variation::VariantI. See Bio::Variation::VariantI for details.

If the variation described by a DNAMutation object is transcibed, link the corresponding Bio::Variation::RNAChange object to it using method RNAChange(). See Bio::Variation::RNAChange for more information.

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 _

CpG

  Title   : CpG
  Usage   : $obj->CpG()
  Function: sets and returns boolean values for variation 
            hitting a CpG site.  Unset value return -1.
  Example : $obj->CpG()
  Returns : boolean
  Args    : optional true of false value
 
 

RNAChange

  Title   : RNAChange
  Usage   : $mutobj = $obj->RNAChange;
          : $mutobj = $obj->RNAChange($objref);
  Function: Returns or sets the link-reference to a mutation/change object.
            If there is no link, it will return undef
  Returns : an obj_ref or undef
 
 

label

  Title   : label
  Usage   : $obj->label();
  Function: 
 
             Sets and returns mutation event label(s).  If value is not
             set, or no argument is given returns false.  Each
             instantiable subclass of L<Bio::Variation::VariantI> needs
             to implement this method. Valid values are listed in
             'Mutation event controlled vocabulary' in
             http://www.ebi.ac.uk/mutations/recommendations/mutevent.html.
 
  Example : 
  Returns : string
  Args    : string
 
 

sysname

  Title   : sysname
  Usage   : $self->sysname
  Function: 
 
            This subroutine creates a string corresponding to the
            'systematic name' of the mutation. Systematic name is
            specified in Antonorakis & MDI Nomenclature Working Group:
            Human Mutation 11:1-3, 1998. 
            
  Returns : string