Bio::EnsEMBL::Variation ConsequenceType
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Summary
Bio::EnsEMBL::Variation::ConsequenceType
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Utils::Exception qw ( warning )
Synopsis
Description
Represents the effect of a Variation in a Transcript
Methods
aa_allelesDescriptionCode
aa_endDescriptionCode
aa_startDescriptionCode
allelesDescriptionCode
cdna_endDescriptionCode
cdna_startDescriptionCode
cds_endDescriptionCode
cds_startDescriptionCode
codonDescriptionCode
display_consequenceDescriptionCode
empty_type
No description
Code
endDescriptionCode
newDescriptionCode
startDescriptionCode
strandDescriptionCode
transcript_idDescriptionCode
typeDescriptionCode
variation_feature_idDescriptionCode
Methods description
aa_allelescode    nextTop
  Arg [1]    : (optional) string $aa_alleles
  Example    : $aa_alleles = $consequence_type->aa_alleles
  Description: Getter/Setter for the aa that changes in the transcript
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : At Risk
aa_endcodeprevnextTop
  Arg [1]    : (optional) int $aa_end
  Example    : $aa_end = $consequence_type->aa_end
  Description: Getter/Setter for the end of the aa in peptide coordinates
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : At Risk
aa_startcodeprevnextTop
  Arg [1]    : (optional) int $aa_start
  Example    : $aa_start = $consequence_type->aa_start
  Description: Getter/Setter for the start of the aa in peptide coordinates
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : At Risk
allelescodeprevnextTop
  Arg [1]    : (optional) array ref $alleles
  Example    : @alleles = @{$consequence_type->alleles};
  Description: Getter/Setter for the alleles for the variation
  Returntype : reference to array
  Exceptions : none
  Caller     : general
  Status     : At Risk
cdna_endcodeprevnextTop
  Arg [1]    : (optional) int $cdna_end
  Example    : $cdna_end = $consequence_type->cdna_end
  Description: Getter/Setter for the end of the variation in cdna coordinates
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : At Risk
cdna_startcodeprevnextTop
  Arg [1]    : (optional) int $cdna_start
  Example    : $cdna_start = $consequence_type->cdna_start
  Description: Getter/Setter for the start of the variation in the cdna coordinates
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : At Risk
cds_endcodeprevnextTop
  Arg [1]    : (optional) int $cds_end
  Example    : $cds_end = $consequence_type->cds_end
  Description: Getter/Setter for the end of the variation in the coding sequence
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : At Risk
cds_startcodeprevnextTop
  Arg [1]    : (optional) int $cds_start
  Example    : $cds_start = $consequence_type->cds_start
  Description: Getter/Setter for the start of the variation in the coding sequence
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : At Risk
codoncodeprevnextTop
  Arg [1]    : (optional) string $codon
  Example    : $codon = $consequence_type->codon
  Description: Getter/Setter for the codon affected by that Allele in the transcript
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : At Risk
display_consequencecodeprevnextTop
  Arg [1]    : (optional) string $consequence_type
  Example    : $display_consequence = $ct->display_consequence();
  Description: Getter for the consequence type to display,
               when more than one
  Returntype : string
  Exceptions : throw on incorrect argument
  Caller     : webteam
  Status     : At Risk
endcodeprevnextTop
  Arg [1]    : (optional) int $end
  Example    : $end = $consequence_type->end
  Description: Getter/Setter for the end of the variation in the sequence
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : At Risk
newcodeprevnextTop
  Arg [1]    : (optional) int $transcript_id
  Arg [2]    : (optional) int $variation_feature_id
  Arg [2]    : (optional) int $start
  Arg [3]    : (optional) int $end
  Arg [4]    : (optional) int $strand
  Arg [5]    : (optional) refarray $alleles
  Example    : $synonym = Bio::EnsEMBL::Variation::ConsequenceType->new($transcript_id,$variation_feature_id,$start,$end,$strand,['A','C']);
  Description: Creates a new ConsequenceType
  Returntype : Bio::EnsEMBL::Variation::ConsequenceType
  Exceptions : none
  Caller     : general
  Status     : At Risk
startcodeprevnextTop
  Arg [1]    : (optional) int $start
  Example    : $start = $consequence_type->start
  Description: Getter/Setter for the start of the variation in the sequence
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : At Risk
strandcodeprevnextTop
  Arg [1]    : (optional) int $strand
  Example    : $strand = $consequence_type->strand
  Description: Getter/Setter for the strand of the variation in the sequence
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : At Risk
transcript_idcodeprevnextTop
  Arg [1]    : (optional) int $transcript_id
  Example    : $transcript_id = $consequence_type->transcript_id;
  Description: Getter/Setter for the internal id of the transcript_id calculated
               the effect of the Variation
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : At Risk
typecodeprevnextTop
  Arg [1]    : string $type 
               (possible types 'FRAMESHIFT_CODING','STOP_GAINED','STOP_LOST','NON_SYNONYMOUS_CODING',
		'SYNONYMOUS_CODING','REGULATORY_REGION','WITHIN_MATURE_miRNA','5PRIME_UTR','3PRIME_UTR','INTRONIC','UPSTREAM','DOWNSTREAM','WITHIN_NON_CODING_GENE','INTERGENIC', 'SARA')
  Example    : $consequence_type = $consequence_type->type
  Description: Getter/Setter for consequence type of the variation in the transcript
  Returntype : none
  Exceptions : warning if the consequence type is not recognised
  Caller     : general
  Status     : At Risk
variation_feature_idcodeprevnextTop
  Arg [1]    : (optional) int $variation_feature_id
  Example    : $variation_feature_id = $consequence_type->variation_feature_id;
  Description: Getter/Setter for the variation_feature affecting the transcript
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : At Risk
Methods code
aa_allelesdescriptionprevnextTop
sub aa_alleles {
  my $self = shift;

  if(@_) {
    $self->{'aa_alleles'} = shift;
  }
  
  return $self->{'aa_alleles'}
}
aa_enddescriptionprevnextTop
sub aa_end {
  my $self = shift;

  if(@_) {
    $self->{'aa_end'} = shift;
  }
  
  return $self->{'aa_end'}
}
aa_startdescriptionprevnextTop
sub aa_start {
  my $self = shift;

  if(@_) {
    $self->{'aa_start'} = shift;
  }
  
  return $self->{'aa_start'}
}
allelesdescriptionprevnextTop
sub alleles {
  my $self = shift;

  if(@_) {
    $self->{'alleles'} = shift;
  }

  return $self->{'alleles'};
}
cdna_enddescriptionprevnextTop
sub cdna_end {
  my $self = shift;

  if(@_) {
    $self->{'cdna_end'} = shift;
  }
  
  return $self->{'cdna_end'}
}
cdna_startdescriptionprevnextTop
sub cdna_start {
  my $self = shift;

  if(@_) {
    $self->{'cdna_start'} = shift;
  }
  
  return $self->{'cdna_start'}
}
cds_enddescriptionprevnextTop
sub cds_end {
  my $self = shift;

  if(@_) {
    $self->{'cds_end'} = shift;
  }
  
  return $self->{'cds_end'}
}
cds_startdescriptionprevnextTop
sub cds_start {
  my $self = shift;

  if(@_) {
    $self->{'cds_start'} = shift;
  }
  
  return $self->{'cds_start'}
}
codondescriptionprevnextTop
sub codon {
  my $self = shift;

  if(@_) {
    $self->{'codon'} = shift;
  }
  
  return $self->{'codon'}
}
display_consequencedescriptionprevnextTop
sub display_consequence {
    my $self = shift;
 
    my $highest_priority;
    #get the value to display from the consequence_type attribute
    $highest_priority = 'INTERGENIC';
    foreach my $ct (@{$self->type}){
	if ($CONSEQUENCE_TYPES{$ct} < $CONSEQUENCE_TYPES{$highest_priority}){
	    $highest_priority = $ct;
	}
    }

    return $highest_priority;
}
empty_typedescriptionprevnextTop
sub empty_type {
    my $self = shift;

    $self->{'type'} = ();
    return $self->type;
}

1;
}
enddescriptionprevnextTop
sub end {
  my $self = shift;

  if(@_) {
    $self->{'end'} = shift;
  }
  
  return $self->{'end'}
}
newdescriptionprevnextTop
sub new {
  my ($caller, $transcript_id, $variation_feature_id, $start, $end, $strand, $alleles) = @_;

  my $class = ref($caller) || $caller;

  return bless( {'transcript_id'   => $transcript_id,
		 'variation_feature_id' => $variation_feature_id,
		 'alleles'  => $alleles,
		 'start' => $start,
		 'end'   => $end,
		 'strand' => $strand}, $class );
}
startdescriptionprevnextTop
sub start {
  my $self = shift;

  if(@_) {
    $self->{'start'} = shift;
  }
  
  return $self->{'start'}
}
stranddescriptionprevnextTop
sub strand {
  my $self = shift;

  if(@_) {
    $self->{'strand'} = shift;
  }
  
  return $self->{'strand'}
}
transcript_iddescriptionprevnextTop
sub transcript_id {
  my $self = shift;

  if(@_) {
    $self->{'transcript_id'} = shift;
  }

  return $self->{'transcript_id'};
}
typedescriptionprevnextTop
sub type {
  my $self = shift;

  if(@_) {
      my $type = shift;
      #there is a special type, SARA, that only applies to the effect of the Alleles, and is equivalent
      #to Same As Reference Allele, which is not stored anywhere in the database and need no conversion at all
      #when creating the VariationFeature object, thus the absence in the hash
      if (defined $CONSEQUENCE_TYPES{$type} || $type eq 'SARA'){
	  push @{$self->{'type'}}, $type;
      }
      else{
	  warning("Trying to set the consequence type to a not valid value. Possible values: ",keys %CONSEQUENCE_TYPES,"\n");
      }
  }
  return $self->{'type'}
}
variation_feature_iddescriptionprevnextTop
sub variation_feature_id {
  my $self = shift;

  if(@_) {
    $self->{'variation_feature_id'} = shift;
  }

  return $self->{'variation_feature_id'};
}
General documentation
No general documentation available.