Bio::LiveSeq::Mutator.3pm

Langue: en

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

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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.