Bio::LiveSeq::Mutator - Package mutating LiveSequences # $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); } 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. 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://bugzilla.bioperl.org/ 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 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.