Bio::Variation DNAMutation
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Summary
Bio::Variation::DNAMutation - DNA level mutation class
Package variables
No package variables defined.
Inherit
Bio::Variation::VariantI
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, "\n"; # 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.
Methods
new
No description
Code
CpGDescriptionCode
_CpG_value
No description
Code
RNAChangeDescriptionCode
labelDescriptionCode
_point_type_label
No description
Code
sysnameDescriptionCode
Methods description
CpGcode    nextTop
 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
RNAChangecodeprevnextTop
 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
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
sysnamecodeprevnextTop
 Title   : sysname
Usage : $self->sysname
Function:
This subroutine creates a string corresponding to the 'systematic name' of the mutation. Systematic name is specified in Antonorakis & MDI Nomenclature Working Group: Human Mutation 11:1-3, 1998. Returns : string
Methods code
newdescriptionprevnextTop
sub new {
    my($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,  $region, $region_value, $region_dist, $numbering, 
	$cpg, $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
				  REGION
				  REGION_VALUE
				  REGION_DIST
				  NUMBERING
				  CPG
				  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);

    $cpg && $self->CpG($cpg);
    
    return $self; # success - we hope!
}
CpGdescriptionprevnextTop
sub CpG {
   my ($obj,$value) = @_;
   if( defined $value) {
       $value ? ($value = 1) : ($value = 0);
       $obj->{'cpg'} = $value;
   }
    elsif (not defined $obj->{'label'}) {
	$obj->{'cpg'} = $obj->_CpG_value;
    }
   else {
       return $obj->{'cpg'};
   }
}
_CpG_valuedescriptionprevnextTop
sub _CpG_value {
    my ($self) = @_;
    if ($self->allele_ori eq $self->allele_mut and length ($self->allele_ori) == 1 ) {
    
	# valid only for point mutations
# CpG methylation-mediated deamination:
# CG -> TG | CG -> CA substitutions
# implementation here is less strict: if CpG dinucleotide was hit
if ( ( ($self->allele_ori eq 'c') && (substr($self->upStreamSeq, 0, 1) eq 'g') ) || ( ($self->allele_ori eq 'g') && (substr($self->dnStreamSeq, -1, 1) eq 'c') ) ) { return 1; } else { return 0; } } else { $self->warn('CpG makes sense only in the context of point mutation'); return; }
}
RNAChangedescriptionprevnextTop
sub RNAChange {
  my ($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, $value) = @_;
    my ($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 (not $o and not $m ) {
	$self->warn("[DNAMutation, label] Both alleles should not be empty!\n");
	$type = 'no change'; # is this enough?
} elsif ($o && $m && length($o) == length($m) && length($o) == 1) { $type = 'point'; $type .= ", ". _point_type_label($o, $m); } elsif (not $o ) { $type = 'insertion'; } elsif (not $m ) { $type = 'deletion'; } else { $type = 'complex'; } $self->{'label'} = $type; return $self->{'label'};
}
_point_type_labeldescriptionprevnextTop
sub _point_type_label {
    my ($o, $m) = @_;
    my ($type);
    my %transition = ('a' => 'g',
		   'g' => 'a',
		   'c' => 't',
		   't' => 'c');
    $o = lc $o;
    $m = lc $m;
    if ($o eq $m) {
	$type = 'no change';
    }
    elsif ($transition{$o} eq $m ) {
	$type = 'transition';
    }
    else {
	$type = 'transversion';
    }
}
sysnamedescriptionprevnextTop
sub sysname {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'sysname'} = $value;
    } else {
	$self->warn('Mutation start position is not defined') 
	    if not defined $self->start;
	my $sysname = '';
	# show the alphabet only if $self->SeqDiff->alphabet is set;
my $mol = ''; if ($self->SeqDiff ) { if ($self->SeqDiff && $self->SeqDiff->alphabet && $self->SeqDiff->alphabet eq 'dna') { $mol = 'g.'; } elsif ($self->SeqDiff->alphabet && $self->SeqDiff->alphabet eq 'rna') { $mol = 'c.'; } } my $sep; if ($self->isMutation) { $sep = '>'; } else { $sep = '|'; } my $sign = '+'; $sign = '' if $self->start < 1; $sysname .= $mol ;#if $mol;
$sysname .= $sign. $self->start; my @alleles = $self->each_Allele; $self->allele_mut($alleles[0]); $sysname .= 'del' if $self->label =~ /deletion/; $sysname .= 'ins' if $self->label =~ /insertion/; $sysname .= uc $self->allele_ori->seq if $self->allele_ori->seq; #push @alleles, $self->allele_mut if $self->allele_mut;
foreach my $allele (@alleles) { $self->allele_mut($allele); $sysname .= $sep if $self->label =~ /point/ or $self->label =~ /complex/; $sysname .= uc $self->allele_mut->seq if $self->allele_mut->seq; } $self->{'sysname'} = $sysname; #$self->{'sysname'} = $sign. $self->start.
# uc $self->allele_ori->seq. $sep. uc $self->allele_mut->seq;
} return $self->{'sysname'}; } 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 _