Bio::Variation RNAChange
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Summary
Bio::Variation::RNAChange - Sequence change class for RNA level
Package variables
No package variables defined.
Included modules
Bio::Tools::CodonTable
Inherit
Bio::Variation::VariantI
Synopsis
   $rnachange = Bio::Variation::RNAChange->new
('-start' => $start,
'-end' => $end,
'-length' => $len,
'-codon_pos' => $cp,
'-upStreamSeq' => $upflank,
'-dnStreamSeq' => $dnflank,
'-proof' => $proof,
'-isMutation' => 1,
'-mut_number' => $mut_number
);
$a1 = Bio::Variation::Allele->new;
$a1->seq('a');
$rnachange->allele_ori($a1);
my $a2 = Bio::Variation::Allele->new;
$a2->seq('t');
$rnachange->add_Allele($a2);
$rnachange->allele_mut($a2);
print "The codon change is ", $rnachange->codon_ori, ">", $rnachange->codon_mut, "\n"; # add it to a SeqDiff container object $seqdiff->add_Variant($rnachange); # and create links to and from DNA level mutation objects $rnachange->DNAMutation($dnamut); $dnamut->RNAChange($rnachange);
Description
The instantiable class Bio::Variation::DNAMutation describes basic
sequence changes at RNA molecule level. It uses methods defined in
superclass Bio::Variation::VariantI. See Bio::Variation::VariantI
for details.
You are normally expected to create a corresponding
Bio::Variation::DNAMutation object even if mutation is defined at
RNA level. The numbering follows then cDNA numbering. Link the
DNAMutation object to the RNAChange object using the method
DNAMutation(). If the variation described by a RNAChange object is
translated, link the corresponding Bio::Variation::AAChange object
to it using method AAChange(). See Bio::Variation::DNAMutation and
Bio::Variation::AAChange for more information.
Methods
new
No description
Code
codon_oriDescriptionCode
codon_mutDescriptionCode
codon_posDescriptionCode
codon_tableDescriptionCode
DNAMutationDescriptionCode
AAChangeDescriptionCode
exons_modifiedDescriptionCode
regionDescriptionCode
cds_endDescriptionCode
labelDescriptionCode
_change_codon_posDescriptionCode
Methods description
codon_oricode    nextTop
 Title   : codon_ori
Usage : $obj->codon_ori();
Function:
Sets and returns codon_ori triplet. If value is not set, creates the codon triplet from the codon position and flanking sequences. The string has to be three characters long. The character content is not checked. Example : Returns : string Args : string
codon_mutcodeprevnextTop
 Title   : codon_mut
Usage : $obj->codon_mut();
Function:
Sets and returns codon_mut triplet. If value is not set, creates the codon triplet from the codon position and flanking sequences. Return undef for other than point mutations. Example : Returns : string Args : string
codon_poscodeprevnextTop
 Title   : codon_pos
Usage : $obj->codon_pos();
Function:
Sets and returns the position of the mutation start in the codon. If value is not set, returns false. Example : Returns : 1,2,3 Args : none if get, the new value if set
codon_tablecodeprevnextTop
 Title   : codon_table
Usage : $obj->codon_table();
Function:
Sets and returns the codon table id of the RNA If value is not set, returns 1, 'universal' code, as the default. Example : Returns : integer Args : none if get, the new value if set
DNAMutationcodeprevnextTop
 Title   : DNAMutation
Usage : $mutobj = $obj->DNAMutation;
: $mutobj = $obj->DNAMutation($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
AAChangecodeprevnextTop
 Title   : AAChange
Usage : $mutobj = $obj->AAChange;
: $mutobj = $obj->AAChange($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
exons_modifiedcodeprevnextTop
 Title   : exons_modified
Usage : $modified = $obj->exons_modified;
: $modified = $obj->exons_modified(1);
Function: Returns or sets information (example: a simple boolean flag) about
the modification of exons as a result of a mutation.
regioncodeprevnextTop
 Title   : region
Usage : $obj->region();
Function:
Sets and returns the name of the sequence region type or protein domain at this location. If value is not set, returns false. Example : Returns : string Args : string
cds_endcodeprevnextTop
 Title   : cds_end
Usage : $cds_end = $obj->get_cds_end();
Function:
Sets or returns the cds_end from the beginning of the DNA sequence to the coordinate start used to describe variants. Should be the location of the last nucleotide of the terminator codon of the gene. Example : Returns : value of cds_end, a scalar Args :
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
_change_codon_poscodeprevnextTop
 Title   : _change_codon_pos
Usage : $newCodonPos = _change_codon_pos($myCodonPos, 5)
Function:
Keeps track of the codon position in a changeing sequence Returns : codon_pos = integer 1, 2 or 3 Args : valid codon position signed integer offset to a new location in sequence
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,
	$mut_number,  $isMutation,
	$codon_ori, $codon_mut, $codon_pos, $codon_table, $cds_end) =
	    $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
				  MUT_NUMBER
				  ISMUTATION
				  CODON_ORI
				  CODON_MUT
				  CODON_POS
				  TRANSLATION_TABLE
				  CDS_END
				  )],@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);
    
    $codon_ori  && $self->codon_ori($codon_ori);
    $codon_mut  && $self->codon_mut($codon_mut);
    $codon_pos  && $self->codon_pos($codon_pos);
    $codon_table && $self->codon_table($codon_table);
    $cds_end  && $self->cds_end($cds_end);
    return $self; # success - we hope!
}
codon_oridescriptionprevnextTop
sub codon_ori {
    my ($self,$value) = @_;
    if (defined $value) {
	if (length $value != 3) {
	    $self->warn("Codon string\" $value\" is not three characters long");
	}
	$self->{'codon_ori'} = $value;
    }
    elsif (! $self->{'codon_ori'}) {
	my $codon_ori = '';

	if ($self->region eq 'coding' && $self->start && $self->start  >= 1) {
	    
	    $self->warn('Codon position is not defined') 
		if not defined $self->codon_pos;
	    $self->warn('Upstream flanking sequence  is not defined') 
		if not defined $self->upStreamSeq;
	    $self->warn('Downstream flanking sequence  is not defined') 
		if not defined $self->dnStreamSeq;

	    my $cpos = $self->codon_pos; 
	    $codon_ori = substr($self->upStreamSeq, -$cpos +1  , $cpos-1);
	    $codon_ori .= substr($self->allele_ori->seq, 0, 4-$cpos) 
		if $self->allele_ori and $self->allele_ori->seq;
	    $codon_ori .= substr($self->dnStreamSeq, 0, 3-length($codon_ori));
	}
	$self->{'codon_ori'} = lc $codon_ori;
    }
    return $self->{'codon_ori'};
}
codon_mutdescriptionprevnextTop
sub codon_mut {
    my ($self,$value) = @_;
    if (defined $value) {
	if (length $value != 3 ) {
	    $self->warn("Codon string\" $value\" is not three characters long");
	}
	$self->{'codon_mut'} = $value;
    }
    else {
	my $codon_mut = '';
	if ($self->allele_ori->seq and $self->allele_mut->seq and
	  CORE::length($self->allele_ori->seq) == 1 and 
	  CORE::length($self->allele_mut->seq) == 1 and
	    $self->region eq 'coding' and $self->start >= 1) {

	    $self->warn('Codon position is not defined') 
		if not defined $self->codon_pos;
	    $self->warn('Upstream flanking sequnce  is not defined') 
		if not defined $self->upStreamSeq;
	    $self->warn('Downstream flanking sequnce  is not defined') 
		if not defined $self->dnStreamSeq;
	    $self->throw('Mutated allele is not defined') 
		if not defined $self->allele_mut;
	    
	    my $cpos = $self->codon_pos;
	    $codon_mut = substr($self->upStreamSeq, -$cpos +1  , $cpos-1);
	    $codon_mut .= substr($self->allele_mut->seq, 0, 4-$cpos) 
		if $self->allele_mut and $self->allele_mut->seq; 
	    $codon_mut .= substr($self->dnStreamSeq, 0, 3-length($codon_mut));
	    
	    $self->{'codon_mut'} = lc $codon_mut;
	}
    }
    return $self->{'codon_mut'};
}
codon_posdescriptionprevnextTop
sub codon_pos {
    my ($self,$value) = @_;
    if( defined $value) {
	if ( $value !~ /[123]/ ) {
	    $self->throw("'$value' is not a valid codon position");
	}
	$self->{'codon_pos'} = $value;
    }
    return $self->{'codon_pos'};
}
codon_tabledescriptionprevnextTop
sub codon_table {
    my ($self,$value) = @_;
    if( defined $value) {
	if (  not $value =~ /^\d$/ ) {
	    $self->throw("'$value' is not a valid codon table ID\n".
			"Has to be a positive integer. Defaulting to 1\n");
	} else {
	    $self->{'codon_table'} = $value;
	}
    }
    if( ! exists $self->{'codon_table'} ) {
	return 1;
    } else {
	return $self->{'codon_table'};
    }
}
DNAMutationdescriptionprevnextTop
sub DNAMutation {
    my ($self,$value) = @_;
    if (defined $value) {
	if( ! $value->isa('Bio::Variation::DNAMutation') ) {
	    $self->throw("Is not a Bio::Variation::DNAMutation object but a [$self]");
	    return;
	}
	else {
	    $self->{'DNAMutation'} = $value;
	}
    }
    unless (exists $self->{'DNAMutation'}) {
	return;
    } else {
	return $self->{'DNAMutation'};
    }
}
AAChangedescriptionprevnextTop
sub AAChange {
    my ($self,$value) = @_;
    if (defined $value) {
	if( ! $value->isa('Bio::Variation::AAChange') ) {
	    $self->throw("Is not a Bio::Variation::AAChange object but a [$self]");
	return;
	}
	else {
	    $self->{'AAChange'} = $value;
	}
    }
    unless (exists $self->{'AAChange'}) {
	return;
    } else {
	return $self->{'AAChange'};
    }
}
exons_modifieddescriptionprevnextTop
sub exons_modified {
  my ($self,$value)=@_;
  if (defined($value)) {
    $self->{'exons_modified'}=$value;
  }
  return ($self->{'exons_modified'});
}
regiondescriptionprevnextTop
sub region {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'region'} = $value;
    } 
    elsif (not defined $self->{'region'}) {

	$self->warn('Mutation start position is not defined') 
	    if not defined $self->start and $self->verbose;
	$self->warn('Mutation end position is not defined') 
	    if not defined $self->end and $self->verbose;
	$self->warn('Length of the CDS is not defined, the mutation can be beyond coding region!')
	    if not defined $self->cds_end and $self->verbose;
	
	$self->region('coding');
	if ($self->end && $self->end < 0 ){
	    $self->region('5\'UTR');
	}
	elsif ($self->start && $self->cds_end && $self->start > $self->cds_end ) {
	    $self->region('3\'UTR');
	}
    }
    return $self->{'region'};
}
cds_enddescriptionprevnextTop
sub cds_end {
    my ($self, $value) = @_;
    if (defined $value) {
	$self->warn("[$value] is not a good value for sequence position") 
	    if not $value =~ /^\d+$/ ;
	$self->{'cds_end'} = $value;
    } else {
	$self->{'cds_end'} = $self->SeqDiff->cds_end if $self->SeqDiff;
    }
    return $self->{'cds_end'};
}
labeldescriptionprevnextTop
sub label {
    my ($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;

    my $ct  = Bio::Tools::CodonTable -> new ( -id => $self->codon_table );
    if ($o and $m and CORE::length($o) == 1 and CORE::length($m) == 1) { 
	if (defined $self->AAChange) {
	    if ($self->start > 0 and $self->start < 4 ) {
		$type = 'initiation codon';
	    }
	    elsif ($self->codon_ori && $ct->is_ter_codon($self->codon_ori) ) {
		#AAChange->allele_ori and $self->AAChange->allele_ori->seq eq '*' ) {
$type = 'termination codon'; } elsif ($self->codon_mut && $ct->is_ter_codon($self->codon_mut) ) { #elsif ($self->AAChange->allele_mut and $self->AAChange->allele_mut->seq eq "*") {
$type = 'nonsense'; } elsif ($o and $m and ($o eq $m or $self->AAChange->allele_ori->seq eq $self->AAChange->allele_mut->seq)) { $type = 'silent'; } else { $type = 'missense'; } } else { $type = 'unknown'; } } else { my $len = 0; $len = CORE::length($o) if $o; $len -= CORE::length($m) if $m; if ($len%3 == 0 ) { $type = 'inframe'; } else { $type = 'frameshift'; } if (not $m ) { $type .= ', '. 'deletion'; } elsif (not $o ) { $type .= ', '. 'insertion'; } else { $type .= ', '. 'complex'; } if ($self->codon_ori && $ct->is_ter_codon($self->codon_ori) ) { $type .= ', '. 'termination codon'; } } $self->{'label'} = $type; return $self->{'label'};
}
_change_codon_posdescriptionprevnextTop
sub _change_codon_pos {
($$)  {    my ($cpos, $i) = @_;

    $cpos = ($cpos + $i%3)%3;
    if ($cpos > 3 ) {
	$cpos = $cpos - 3;
    }
    elsif ($cpos < 1 ) {
	$cpos = $cpos + 3;
    }
    return $cpos;
}

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 _