Bio::Variation AAChange
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Summary
Bio::Variation::AAChange - Sequence change class for polypeptides
Package variables
No package variables defined.
Inherit
Bio::Variation::VariantI
Synopsis
   $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);
Description
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.
Methods
BEGIN Code
 + _matrix  
new
No description
Code
RNAChangeDescriptionCode
labelDescriptionCode
similarity_scoreDescriptionCode
trivnameDescriptionCode
Methods description
BEGINcodeTop
RNAChangecode    nextTop
 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
labelcodeprevnextTop
 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 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
similarity_scorecodeprevnextTop
 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
trivnamecodeprevnextTop
 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
Methods code
BEGINTop
BEGIN {
my $matrix = << "__MATRIX__";
# Matrix made by matblas from blosum62.iij
# * column uses minimum score
# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
# Blocks Database = /data/blocks_5.0/blocks.dat
# Cluster Percentage: >= 62
# Entropy = 0.6979, Expected = -0.5209
A R N D C Q E G H I L K M F P S T W Y V B Z X *
A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4
R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -4
N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4
D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 -4
C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4
Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -4
E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4
G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -4
H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 -4
I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3 -3 -3 -1 -4
L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -4 -3 -1 -4
K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -4
M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -1 -1 -4
F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1 -4
P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -1 -2 -4
S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -4
T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0 -1 -1 0 -4
W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3 -4 -3 -2 -4
Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1 -4
V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -4
B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -4
Z -1 0 0 1 -3 3 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4
X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -4
* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1
__MATRIX__
my %blosum = (); $matrix =~ /^ +(.+)$/m; my @aas = split / +/, $1; foreach my $aa (@aas) { my $tmp = $aa; $tmp = "\\$aa" if $aa eq '*'; $matrix =~ /^($tmp) +([-+]?\d.*)$/m; my @scores = split / +/, $2 if defined $2; my $count = 0; foreach my $ak (@aas) { $blosum{$aa}->{$aas[$count]} = $scores[$count]; $count++; } } sub _matrix; $MATRIX =\% blosum;
}
newdescriptionprevnextTop
sub new {
    my($class,@args) = @_;
    my $self = $class->SUPER::new(@args);

    my ($start, $end, $length, $strand, $primary, $source,
	$frame, $score, $gff_string,
	$allele_ori,  $allele_mut,  $upstreamseq,  $dnstreamseq,
	$label,  $status,  $proof,  $re_changes,  $region, $region_value,
        $region_dist,
	$numbering,  $mut_number,  $ismutation) =
	    $self->_rearrange([qw(START
				  END
				  LENGTH
				  STRAND
				  PRIMARY
				  SOURCE
				  FRAME
				  SCORE
				  GFF_STRING
				  ALLELE_ORI
				  ALLELE_MUT
				  UPSTREAMSEQ
				  DNSTREAMSEQ
				  LABEL
				  STATUS
				  PROOF
				  RE_CHANGES
				  REGION
				  REGION_VALUE
				  REGION_DIST
				  NUMBERING
				  MUT_NUMBER
				  ISMUTATION
				  )],@args);

    $self->primary_tag("Variation");

    $self->{ 'alleles' } = [];

    $start && $self->start($start);
    $end   && $self->end($end);
    $length && $self->length($length);
    $strand && $self->strand($strand);
    $primary && $self->primary_tag($primary);
    $source  && $self->source_tag($source);
    $frame   && $self->frame($frame);
    $score   && $self->score($score);
    $gff_string && $self->_from_gff_string($gff_string);

    $allele_ori && $self->allele_ori($allele_ori);
    $allele_mut  && $self->allele_mut($allele_mut);
    $upstreamseq  && $self->upstreamseq($upstreamseq);
    $dnstreamseq  && $self->dnstreamseq($dnstreamseq);

    $label  && $self->label($label);
    $status  && $self->status($status);
    $proof && $self->proof($proof);
    $region  && $self->region($region);
    $region_value  && $self->region_value($region_value);
    $region_dist  && $self->region_dist($region_dist);
    $numbering && $self->numbering($numbering);
    $mut_number && $self->mut_number($mut_number);
    $ismutation && $self->isMutation($ismutation);

    return $self; # success - we hope!
}
RNAChangedescriptionprevnextTop
sub RNAChange {
  my ($self,$value) = @_;
  if (defined $value) {
      if( ! $value->isa('Bio::Variation::RNAChange') ) {
	  $self->throw("Is not a Bio::Variation::RNAChange object but a [$self]");
	  return;
      }
      else {
	  $self->{'RNAChange'} = $value;
      }
  }
  unless (exists $self->{'RNAChange'}) {
      return;
  } else {
      return $self->{'RNAChange'};
  }
}
labeldescriptionprevnextTop
sub label {
    my ($self) = @_;
    my ($o, $m, $type);
    $o = $self->allele_ori->seq if $self->allele_ori and $self->allele_ori->seq;
    $m = $self->allele_mut->seq if $self->allele_mut and $self->allele_mut->seq;

    if ($self->start == 1 ) {
	if ($o and substr($o, 0, 1) ne substr($m, 0, 1)) {
	    $type = 'no translation';
	}
	elsif ($o and $m and $o eq $m ) {
	    $type = 'silent';
	}
	# more ...
} elsif ($o and substr($o, 0, 1) eq '*' ) { if ($m and substr($o, 0, 1) ne substr($m, 0, 1)) { $type = 'post-elongation'; } elsif ($m and $o eq $m ) { $type = 'silent, conservative'; } } elsif ($o and $m and $o eq $m) { $type = 'silent, conservative'; } elsif ($m and $m eq '*') { $type = 'truncation'; } elsif ($o and $m and $o eq $m) { $type = 'silent, conservative'; } elsif (not $m or ($o and $m and length($o) > length($m) and substr($m, -1, 1) ne '*')) { $type = 'deletion'; if ($o and $m and $o !~ $m and $o !~ $m) { $type .= ', complex'; } } elsif (not $o or ($o and $m and length($o) < length($m) and substr($m, -1, 1) ne '*' ) ) { $type = 'insertion'; if ($o and $m and $o !~ $m and $o !~ $m) { $type .= ', complex'; } } elsif ($o and $m and $o ne $m and length $o == 1 and length $m == 1 ) { $type = 'substitution'; my $value = $self->similarity_score; if (defined $value) { my $cons = ($value < 0) ? 'nonconservative' : 'conservative'; $type .= ", ". $cons; } } else { $type = 'out-of-frame translation, truncation'; } $self->{'label'} = $type; return $self->{'label'};
}
similarity_scoredescriptionprevnextTop
sub similarity_score {
    my ($self) = @_;
    my ($o, $m, $type);
    $o = $self->allele_ori->seq if $self->allele_ori and $self->allele_ori->seq;
    $m = $self->allele_mut->seq if $self->allele_mut and $self->allele_mut->seq;
    return unless $o and $m and length $o == 1 and length $m == 1;
    return unless $o =~ /[ARNDCQEGHILKMFPSTWYVBZX*]/i and
	$m =~ /[ARNDCQEGHILKMFPSTWYVBZX*]/i;
    return $MATRIX->{"\U$o"}->{"\U$m"};
}
trivnamedescriptionprevnextTop
sub trivname {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'trivname'} = $value;
    } else {
	my ( $aaori, $aamut,$aamutsymbol, $aatermnumber, $aamutterm) =
	    ('', '', '', '', '');
	my $o = $self->allele_ori->seq if $self->allele_ori and $self->allele_ori->seq;
	#my $m = $self->allele_mut->seq if $self->allele_mut and $self->allele_mut->seq;
$aaori = substr ($o, 0, 1) if $o; $aaori =~ tr/\*/X/; my $sep; if ($self->isMutation) { $sep = '>'; } else { $sep = '|'; } my $trivname = $aaori. $self->start; $trivname .= $sep if $sep eq '|'; my @alleles = $self->each_Allele; foreach my $allele (@alleles) { my $m = $allele->seq if $allele->seq; $self->allele_mut($allele); #$trivname .= $sep. uc $m if $m;
$aamutterm = substr ($m, -1, 1) if $m; if ($self->RNAChange->label =~ /initiation codon/ and ( $o and $m and $o ne $m)) { $aamut = 'X'; } elsif (CORE::length($o) == 1 and CORE::length($m) == 1 ) { $aamutsymbol = ''; $aamut = $aamutterm; } elsif ($self->RNAChange->label =~ /deletion/) { $aamutsymbol = 'del'; if ($aamutterm eq '*') { $aatermnumber = $self->start + length($m) -1; $aamut = 'X'. $aatermnumber; } if ($self->RNAChange && $self->RNAChange->label =~ /inframe/){ $aamut = '-'. length($self->RNAChange->allele_ori->seq)/3 ;
} } elsif ($self->RNAChange->label =~ /insertion/) { $aamutsymbol = 'ins'; if (($aamutterm eq '*') && (length($m)-1 != 0)) { $aatermnumber = $self->start + length($m)-1; $aamut = $aatermnumber. 'X'; } if ($self->RNAChange->label =~ /inframe/){ $aamut = '+'. int length($self->RNAChange->allele_mut->seq)/3 ;
} } elsif ($self->RNAChange->label =~ /complex/ ) { my $diff = length($m) - length($o); if ($diff >= 0 ) { $aamutsymbol = 'ins'; } else { $aamutsymbol = 'del' ; } if (($aamutterm eq '*') && (length($m)-1 != 0)) { $aatermnumber = $self->start + length($m)-1; $aamut = $aatermnumber. 'X'; } if ($self->RNAChange->label =~ /inframe/){ if ($diff >= 0 ) { $aamut = '+'. $diff ; } else { $aamut = $diff ; } } } elsif ($self->label =~ /truncation/) { $aamut = $m; } else { $aamutsymbol = ''; $aamut = $aamutterm; } $aamut =~ tr/\*/X/; $trivname .= $aamutsymbol. $aamut. $sep; } chop $trivname; $self->{'trivname'} = $trivname; } return $self->{'trivname'}; } 1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 LehvaslaihoTop
Email: heikki-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _