/ 
bioperl-0.7.0
/ Bio::Variation::RNAChange

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.

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().

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://bio.perl.org/MailList.html             - About the mailing lists

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 email or the web:

bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/

AUTHOR - Heikki Lehvaslaiho

Email: heikki@ebi.ac.uk Address:

EMBL Outstation, European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambs. CB10 1SD, United Kingdom

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

region_value

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

           Sets and returns the name of the sequence region_value type or
           protein domain at this location. Not a valid method for RNAChange.
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