The London Perl and Raku Workshop takes place on 26th Oct 2024. If your company depends on Perl, please consider sponsoring and/or attending.
 / 
bioperl-0.7.2
++
/ Bio::LiveSeq::Mutator

NAME

Bio::LiveSeq::Mutator - Package mutating LiveSequences

SYNOPSIS

  # $gene is a Bio::LiveSeq::Gene object
  my $mutate = Bio::LiveSeq::Mutator->new('-gene' => $gene,
                                          '-numbering' => "coding"
                                           );
  # $mut is a Bio::LiveSeq::Mutation object
  $mutate->add_Mutation($mut);
  # $results is a Bio::Variation::SeqDiff object
  my $results=$mutate->change_gene();
  if ($results) {
      my $out = Bio::Variation::IO->new( '-format' => 'flat');
      $out->write($results);
  }

DESCRIPTION

  This class mutates L<Bio::LiveSeq::Gene> objects and returns a
  L<Bio::Variation::SeqDiff> object. Mutations are described as
  L<Bio::LiveSeq::Mutation> objects.

FEEDBACK

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 & Joseph A.L. Insana

  Email:  heikki@ebi.ac.uk
          insana@ebi.ac.uk, jinsana@gmx.net

  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 _

gene

 Title   : gene
 Usage   : $mutobj = $obj->gene;
         : $mutobj = $obj->gene($objref);
 Function:

           Returns or sets the link-reference to a
           L<Bio::LiveSeq::Gene> object. If no value has ben set, it
           will return undef

 Returns : an object reference  or undef
 Args    : a L<Bio::LiveSeq::Gene>

numbering

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

            Sets and returns coordinate system used in positioning the
            mutations. See L<change_gene> for details.

 Example :
 Returns : string
 Args    : string (coding [transcript number] | gene | entry)

add_Mutation

 Title   : add_Mutation
 Usage   : $self->add_Mutation($ref)
 Function: adds a L<Bio::Liveseq::Mutation> object
 Example :
 Returns :
 Args    : a L<Bio::Liveseq::Mutation>

each_Mutation

 Title   : each_Mutation
 Usage   : foreach $ref ( $a->each_Mutation )
 Function: gets an array of L<Bio::Liveseq::Mutation> objects
 Example :
 Returns : array of Mutations
 Args    :

mutation

 Title   : mutation
 Usage   : $mutobj = $obj->mutation;
         : $mutobj = $obj->mutation($objref);
 Function:

           Returns or sets the link-reference to the current mutation
           object.  If the value is not set, it will return undef.
           Internal method.

 Returns : an object reference  or undef

DNA

 Title   : DNA
 Usage   : $mutobj = $obj->DNA;
         : $mutobj = $obj->DNA($objref);
 Function:

           Returns or sets the reference to the LiveSeq object holding
           the reference sequence. If there is no link, it will return
           undef.
           Internal method.

 Returns : an object reference or undef

RNA

 Title   : RNA
 Usage   : $mutobj = $obj->RNA;
         : $mutobj = $obj->RNA($objref);
 Function:

           Returns or sets the reference to the LiveSeq object holding
           the reference sequence. If the value is not set, it will return
           undef.
           Internal method.

 Returns : an object reference  or undef

dnamut

 Title   : dnamut
 Usage   : $mutobj = $obj->dnamut;
         : $mutobj = $obj->dnamut($objref);
 Function:

           Returns or sets the reference to the current DNAMutation object.
           If the value is not set, it will return undef.
           Internal method.

 Returns : an L<Bio::Variation::DNAMutation> or undef

rnachange

 Title   : rnachange
 Usage   : $mutobj = $obj->rnachange;
         : $mutobj = $obj->rnachange($objref);
 Function:

           Returns or sets the reference to the current RNAChange object.
           If the value is not set, it will return undef.
           Internal method.

 Returns : an L<Bio::Variation::RNAChange> or undef

aachange

 Title   : aachange
 Usage   : $mutobj = $obj->aachange;
         : $mutobj = $obj->aachange($objref);
 Function:

           Returns or sets the reference to the current AAChange object.
           If the value is not set, it will return undef.
           Internal method.

 Returns : an L<Bio::Variation::AAChange> or undef

exons

 Title   : exons
 Usage   : $mutobj = $obj->exons;
         : $mutobj = $obj->exons($objref);
 Function:

           Returns or sets the reference to a current array of Exons.
           If the value is not set, it will return undef.
           Internal method.

 Returns : an array of L<Bio::LiveSeq::Exon> objects or undef

change_gene

 Title   : change_gene
 Usage   : my $mutate = Bio::LiveSeq::Mutator->new(-gene => $gene,
                                                   numbering => "coding"
                                                   );
           # $mut is Bio::LiveSeq::Mutation object
           $mutate->add_Mutation($mut);
           my $results=$mutate->change_gene();

 Function:

           Returns a Bio::Variation::SeqDiff object containing the
           results of the changes performed according to the
           instructions present in Mutation(s).  The -numbering
           argument decides what molecule is being changed and what
           numbering scheme being used:

            -numbering => "entry"

               determines the DNA level, using the numbering from the
               beginning of the sequence

            -numbering => "coding"

               determines the RNA level, using the numbering from the
               beginning of the 1st transcript

               Alternative transcripts can be used by specifying
               "coding 2" or "coding 3" ...

            -numbering => "gene"

               determines the DNA level, using the numbering from the
               beginning of the 1st transcript and inluding introns.
               The meaning equals 'coding' if the reference molecule
               is cDNA.

 Args    : Bio::LiveSeq::Gene object
           Bio::LiveSeq::Mutation object(s)
           string specifying a numbering scheme (defaults to 'coding')
 Returns : Bio::Variation::SeqDiff object or 0 on error

_mutationpos2label

 Title   : _mutationpos2label
 Usage   :
 Function: converts mutation positions into labels
 Example :
 Returns : number of valid mutations
 Args    : LiveSeq sequence object

_set_DNAMutation

 Title   : _set_DNAMutation
 Usage   :
 Function:

           Stores DNA level mutation attributes before mutation into
           L<Bio::Variation::DNAMutation> object.  Links it to SeqDiff
           object.

 Example :
 Returns : L<Bio::Variation::DNAMutation> object
 Args    : L<Bio::Variation::SeqDiff> object

_set_effects

 Title   : _set_effects
 Usage   :
 Function:

           Stores RNA and AA level mutation attributes before mutation
           into L<Bio::Variation::RNAChange> and
           L<Bio::Variation::AACange> objects.  Links them to
           SeqDiff object.

 Example :
 Returns :
 Args    : L<Bio::Variation::SeqDiff> object
           L<Bio::Variation::DNAMutation> object

_untranslated

 Title   : _untranslated
 Usage   :
 Function:

           Stores RNA change attributes before mutation
           into L<Bio::Variation::RNAChange object.  Links it to
           SeqDiff object.

 Example :
 Returns :
 Args    : L<Bio::Variation::SeqDiff> object
           L<Bio::Variation::DNAMutation> object