Bio::Variation::RNAChange.3pm

Langue: en

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

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Variation::RNAChange - Sequence change class for RNA level

SYNOPSIS

    $rnachange = Bio::Variation::RNAChange->new
        ('-start'         => $start,
         '-end'           => $end,
         '-length'        => $len,
         '-codon_pos'     => $cp,
         '-upStreamSeq'   => $upflank,
         '-dnStreamSeq'   => $dnflank,
         '-proof'         => $proof,
         '-isMutation'    => 1,
         '-mut_number'    => $mut_number
        );
    $a1 = Bio::Variation::Allele->new;
    $a1->seq('a');
    $rnachange->allele_ori($a1);
    my $a2 = Bio::Variation::Allele->new;
    $a2->seq('t');
    $rnachange->add_Allele($a2);
    $rnachange->allele_mut($a2);
 
    print "The codon change is ", $rnachange->codon_ori, 
        ">", $rnachange->codon_mut, "\n"; 
 
    # add it to a SeqDiff container object
    $seqdiff->add_Variant($rnachange);
 
    # and create links to and from DNA level mutation objects
    $rnachange->DNAMutation($dnamut);
    $dnamut->RNAChange($rnachange);
 
 

DESCRIPTION

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

You are normally expected to create a corresponding Bio::Variation::DNAMutation object even if mutation is defined at RNA level. The numbering follows then cDNA numbering. Link the DNAMutation object to the RNAChange object using the method DNAMutation(). If the variation described by a RNAChange object is translated, link the corresponding Bio::Variation::AAChange object to it using method AAChange(). See Bio::Variation::DNAMutation and Bio::Variation::AAChange 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 _

codon_ori

  Title   : codon_ori
  Usage   : $obj->codon_ori();
  Function: 
 
             Sets and returns codon_ori triplet.  If value is not set,
             creates the codon triplet from the codon position and
             flanking sequences.  The string has to be three characters
             long. The character content is not checked.
 
  Example : 
  Returns : string
  Args    : string
 
 

codon_mut

  Title   : codon_mut
  Usage   : $obj->codon_mut();
  Function: 
 
             Sets and returns codon_mut triplet.  If value is not
             set, creates the codon triplet from the codon position and
             flanking sequences. Return undef for other than point mutations.
 
  Example : 
  Returns : string
  Args    : string
 
 

codon_pos

  Title   : codon_pos
  Usage   : $obj->codon_pos();
  Function: 
 
             Sets and returns the position of the mutation start in the
             codon. If value is not set, returns false.
 
  Example : 
  Returns : 1,2,3
  Args    : none if get, the new value if set
 
 

codon_table

  Title   : codon_table
  Usage   : $obj->codon_table();
  Function: 
 
             Sets and returns the codon table id of the RNA
             If value is not set, returns 1, 'universal' code, as the default.
 
  Example : 
  Returns : integer
  Args    : none if get, the new value if set
 
 

DNAMutation

  Title   : DNAMutation
  Usage   : $mutobj = $obj->DNAMutation;
          : $mutobj = $obj->DNAMutation($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
 
 

AAChange

  Title   : AAChange
  Usage   : $mutobj = $obj->AAChange;
          : $mutobj = $obj->AAChange($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
 
 

exons_modified

  Title   : exons_modified
  Usage   : $modified = $obj->exons_modified;
          : $modified = $obj->exons_modified(1);
  Function: Returns or sets information (example: a simple boolean flag) about
            the modification of exons as a result of a mutation.
 
 

region

  Title   : region
  Usage   : $obj->region();
  Function: 
 
             Sets and returns the name of the sequence region type or
             protein domain at this location.  If value is not set,
             returns false.
 
  Example : 
  Returns : string
  Args    : string
 
 

cds_end

  Title   : cds_end
  Usage   : $cds_end = $obj->get_cds_end();
  Function: 
 
            Sets or returns the cds_end from the beginning of the DNA sequence
            to the coordinate start used to describe variants.
            Should be the location of the last nucleotide of the
            terminator codon of the gene.
 
  Example : 
  Returns : value of cds_end, a scalar
  Args    :
 
 

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
 
 

_change_codon_pos

  Title   : _change_codon_pos
  Usage   : $newCodonPos = _change_codon_pos($myCodonPos, 5)
  Function: 
 
            Keeps track of the codon position in a changeing sequence
 
  Returns : codon_pos = integer 1, 2 or 3
  Args    : valid codon position 
            signed integer offset to a new location in sequence