| Bio::Variation::AAChange(3pm) | User Contributed Perl Documentation | Bio::Variation::AAChange(3pm) |
Bio::Variation::AAChange - Sequence change class for polypeptides
$aamut = Bio::Variation::AAChange->new
('-start' => $start,
'-end' => $end,
'-length' => $len,
'-proof' => $proof,
'-isMutation' => 1,
'-mut_number' => $mut_number
);
my $a1 = Bio::Variation::Allele->new;
$a1->seq($ori) if $ori;
$aamut->allele_ori($a1);
my $a2 = Bio::Variation::Allele->new;
$a2->seq($mut) if $mut;
$aachange->add_Allele($a2);
$aachange->allele_mut($a2);
print "\n";
# add it to a SeqDiff container object
$seqdiff->add_Variant($rnachange);
# and create links to and from RNA level variant objects
$aamut->RNAChange($rnachange);
$rnachange->AAChange($rnachange);
The instantiable class Bio::Variation::RNAChange describes basic sequence changes at polypeptide level. It uses methods defined in superclass Bio::Variation::VariantI, see Bio::Variation::VariantI for details.
If the variation described by a AAChange object has a known Bio::Variation::RNAAChange object, create the link with method AAChange(). See Bio::Variation::AAChange 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 : RNAChange
Usage : $mutobj = $self->RNAChange;
: $mutobj = $self->RNAChange($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 : similarity_score
Usage : $self->similarity_score
Function: Measure for evolutionary conservativeness
of single amino substitutions. Uses BLOSUM62.
Negative numbers are noncoservative changes.
Returns : integer, undef if not single amino acid change
Title : trivname
Usage : $self->trivname
Function:
Given a Bio::Variation::AAChange object with linked
Bio::Variation::RNAChange and Bio::Variation::DNAMutation
objects, this subroutine creates a string corresponding to
the 'trivial name' of the mutation. Trivial name is
specified in Antonorakis & MDI Nomenclature Working Group:
Human Mutation 11:1-3, 1998.
Returns : string
| 2021-03-04 | perl v5.32.1 |