| Bio::LiveSeq::Mutator(3pm) | User Contributed Perl Documentation | Bio::LiveSeq::Mutator(3pm) |
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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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.
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)
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.
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.
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
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
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
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.
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.
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.
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.
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.
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
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
Title : _mutationpos2label Usage : Function: converts mutation positions into labels Example : Returns : number of valid mutations Args : LiveSeq sequence object
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.
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.
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.
| 2018-10-27 | perl v5.26.2 |