Bio::LiveSeq::Mutator(3)

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 Bio::LiveSeq::Gene objects and returns a Bio::Variation::SeqDiff object. Mutations are described as Bio::LiveSeq::Mutation objects. See Bio::LiveSeq::Gene, Bio::Variation::SeqDiff, and Bio::LiveSeq::Mutation for details.

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://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:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Heikki Lehvaslaiho & Joseph A.L. Insana
  Email:  heikki-at-bioperl-dot-org
          insana@ebi.ac.uk, jinsana@gmx.net

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
           Bio::LiveSeq::Gene object. If no value has ben set, it
           will return undef

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

See Bio::LiveSeq::Gene for more information.

  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 Bio::LiveSeq::Mutation object
 Example :
 Returns :
 Args    : a Bio::LiveSeq::Mutation

See Bio::LiveSeq::Mutation for more information.

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

See Bio::LiveSeq::Mutation for more information.

  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 : a Bio::Variation::DNAMutation object or undef

See Bio::Variation::DNAMutation for more information.

  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 : a Bio::Variation::RNAChange object or undef

See Bio::Variation::RNAChange for more information.

  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 : a Bio::Variation::AAChange object or undef

See Bio::Variation::AAChange for more information.

  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 Bio::LiveSeq::Exon objects or undef

See Bio::LiveSeq::Exon for more information.

  change_gene_with_alignment
 Title   : change_gene_with_alignment
 Usage   : $results=$mutate->change_gene_with_alignment($aln);

 Function:

           Returns a Bio::Variation::SeqDiff object containing the
           results of the changes in the alignment. The alignment has
           to be pairwise and have one sequence named 'QUERY', the
           other one is assumed to be a part of the sequence from
           $gene.

           This method offers a shortcut to change_gene and
           automates the creation of Bio::LiveSeq::Mutation objects.
           Use it with almost identical sequnces, e.g. to locate a SNP.

 Args    : Bio::SimpleAlign object representing a short local alignment
 Returns : Bio::Variation::SeqDiff object or 0 on error

See Bio::LiveSeq::Mutation, Bio::SimpleAlign, and Bio::Variation::SeqDiff for more information.

  create_mutation
 Title   : create_mutation
 Usage   :
 Function:

           Formats sequence differences from two sequences into
           Bio::LiveSeq::Mutation objects which can be applied to a
           gene.

           To keep it generic, sequence arguments need not to be
           Bio::LocatableSeq. Coordinate change to parent sequence
           numbering needs to be done by the calling code.

           Called from change_gene_with_alignment

 Args    : Bio::PrimarySeqI inheriting object for the reference sequence
           Bio::PrimarySeqI inheriting object for the query sequence
           integer for the start position of the local sequence difference
           integer for the length of the sequence difference
 Returns : Bio::LiveSeq::Mutation object

  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
           Bio::Variation::DNAMutation object.  Links it to SeqDiff
           object.

 Example :
 Returns : Bio::Variation::DNAMutation object
 Args    : Bio::Variation::SeqDiff object

See Bio::Variation::DNAMutation and Bio::Variation::SeqDiff.

  _set_effects
 Title   : _set_effects
 Usage   :
 Function:

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

 Example :
 Returns :
 Args    : Bio::Variation::SeqDiff object
           Bio::Variation::DNAMutation object

See Bio::Variation::RNAChange, Bio::Variation::RNAChange, Bio::Variation::SeqDiff, and Bio::Variation::DNAMutation.

  _untranslated
 Title   : _untranslated
 Usage   :
 Function:

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

 Example :
 Returns :
 Args    : Bio::Variation::SeqDiff object
           Bio::Variation::DNAMutation object

See Bio::Variation::RNAChange, Bio::Variation::SeqDiff and Bio::Variation::DNAMutation for details.