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