Bio::Variation::DNAMutation(3pm) User Contributed Perl Documentation Bio::Variation::DNAMutation(3pm)
NAME
Bio::Variation::DNAMutation - DNA level mutation class
SYNOPSIS
$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, "
";
# add it to a SeqDiff container object
$seqdiff->add_Variant($dnamut);
DESCRIPTION
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.
FEEDBACK
Mailing Lists
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:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Heikki Lehvaslaiho
Email: heikki-at-bioperl-dot-org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
CpG
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
RNAChange
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
label
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
sysname
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
perl v5.14.2 2012-03-02 Bio::Variation::DNAMutation(3pm)