| Bio::Variation::DNAMutation(3pm) | User Contributed Perl Documentation | Bio::Variation::DNAMutation(3pm) |
Bio::Variation::DNAMutation - DNA level mutation class
$dnamut = Bio::Variation::DNAMutation->new
('-start' => $start,
'-end' => $end,
'-length' => $len,
'-upStreamSeq' => $upflank,
'-dnStreamSeq' => $dnflank,
'-proof' => $proof,
'-isMutation' => 1,
'-mut_number' => $mut_number
);
$a1 = Bio::Variation::Allele->new;
$a1->seq('a');
$dnamut->allele_ori($a1);
my $a2 = Bio::Variation::Allele->new;
$a2->seq('t');
$dnamut->add_Allele($a2);
print "Restriction changes are ", $dnamut->restriction_changes, "\n";
# add it to a SeqDiff container object
$seqdiff->add_Variant($dnamut);
The instantiable class Bio::Variation::DNAMutation describes basic sequence changes in genomic DNA level. It uses methods defined in superclass Bio::Variation::VariantI. See Bio::Variation::VariantI for details.
If the variation described by a DNAMutation object is transcibed, link the corresponding Bio::Variation::RNAChange object to it using method RNAChange(). See Bio::Variation::RNAChange for more information.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : CpG
Usage : $obj->CpG()
Function: sets and returns boolean values for variation
hitting a CpG site. Unset value return -1.
Example : $obj->CpG()
Returns : boolean
Args : optional true of false value
Title : RNAChange
Usage : $mutobj = $obj->RNAChange;
: $mutobj = $obj->RNAChange($objref);
Function: Returns or sets the link-reference to a mutation/change object.
If there is no link, it will return undef
Returns : an obj_ref or undef
Title : label
Usage : $obj->label();
Function:
Sets and returns mutation event label(s). If value is not
set, or no argument is given returns false. Each
instantiable subclass of L<Bio::Variation::VariantI> needs
to implement this method. Valid values are listed in
'Mutation event controlled vocabulary' in
http://www.ebi.ac.uk/mutations/recommendations/mutevent.html.
Example :
Returns : string
Args : string
Title : sysname
Usage : $self->sysname
Function:
This subroutine creates a string corresponding to the
'systematic name' of the mutation. Systematic name is
specified in Antonorakis & MDI Nomenclature Working Group:
Human Mutation 11:1-3, 1998.
Returns : string
| 2021-12-02 | perl v5.32.1 |