Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils ExonExtended
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Summary
Bio::EnsEMBL::Analysis:Tools::GeneBuildUtils::ExonExtended;
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Exon
Bio::EnsEMBL::Feature
Bio::EnsEMBL::Root
Bio::EnsEMBL::Utils::Exception qw ( throw warning )
Inherit
Bio::EnsEMBL::Exon Bio::EnsEMBL::Feature
Synopsis
No synopsis!
Description
This module extends a Bio::EnsEMBL::Transcript with smoe other
methods. You have to re-bless your Bio::EnsEMBL::Transcript objects
to use it.
Methods
biotypeDescriptionCode
clusterDescriptionCode
ev_setDescriptionCode
get_percentage_exon_conversation_in_exon_clusterDescriptionCode
is_3prim_exonDescriptionCode
is_5prim_exonDescriptionCode
is_terminal_exonDescriptionCode
new
No description
Code
next_exonDescriptionCode
number_exons
No description
Code
prev_exonDescriptionCode
transcriptDescriptionCode
visitedDescriptionCode
Methods description
biotype code    nextTop
   Name       : biotype 
   Arg        : String
   Func       : getter/setter for the biotype to which this Exon belongs to 
   Returntype : String describing biotype
clustercodeprevnextTop
   Name       : cluster
   Arg        : Bio::EnsEMBL::Transcript
   Func       : getter/setter for the Bio::EnsEMBL::Transcript the Exon belongs to 
   Returntype : Bio::EnsEMBL::Transcript
ev_setcodeprevnextTop
   Name       : ev_set
   Arg        : String
   Func       : getter/setter for the evidence-set 
   Returntype : String describing ev_set (defined in GeneBuild/TrancriptCoalescer.pm)
get_percentage_exon_conversation_in_exon_cluster() codeprevnextTop
  Example    : $self->get_percentage_exon_conversation_in_exon_cluster
  Arg        : none
  Function   : returns the precentage of other Exons in the same cluster which 
               share the same Exon-boundaries. 
  Returntype : float
is_3prim_exoncodeprevnextTop
   Name       : is_3prim_exon 
   Arg        : none
   Func       : returns 1 if exon is at 3prim end of transcript 
   Returntype : int (0 || 1)
is_5prim_exoncodeprevnextTop
   Name       : is_5prim_exon 
   Arg        : none 
   Func       : returns 1 if exon is at 5prim end of transcript 
   Returntype : int (0 || 1)
is_terminal_exoncodeprevnextTop
   Name       : is_terminal_exon 
   Arg        : none 
   Func       : returns 1 if exon is terminal and 0 othewise 
   Returntype : int (0 || 1)
next_exoncodeprevnextTop
   Name       : next_exon  
   Arg        : Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::ExonExtended; 
   Func       : points to next exon (3'prim) 
   Returntype : Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::ExonExtended;
prev_exoncodeprevnextTop
   Name       : prev_exon 
   Arg        : Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::ExonExtended; 
   Func       : points to previous exon (5'prim) 
   Returntype : Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::ExonExtended;
transcriptcodeprevnextTop
   Name       : transcript 
   Arg        : Bio::EnsEMBL::Transcript
   Func       : getter/setter for the Bio::EnsEMBL::Transcript the Exon belongs to 
   Returntype : Bio::EnsEMBL::Transcript
visited ( $val ) codeprevnextTop
  Function   : marks if exon has been visited in recursion procedure or not 
  Arg        : integer (true / false ) 
  Returntype : integer (true || false ) 
  Caller     : recursion procedure in Condense_EST.pm
Methods code
biotypedescriptionprevnextTop
sub biotype {
  my ($self,$value) = @_;
  if (defined($value)) {
    $self->{'type'} = $value;
  }
  return $self->{'type'};
}
clusterdescriptionprevnextTop
sub cluster {
  my ($self,$value) = @_;
  if (defined($value)) {
    $self->{'cluster'} = $value;
  }
  return $self->{'cluster'};
}
ev_setdescriptionprevnextTop
sub ev_set {
  my ($self,$value) = @_;
  if (defined($value)) {
    $self->{'set'} = $value;
  }
  return $self->{'set'};
}
get_percentage_exon_conversation_in_exon_clusterdescriptionprevnextTop
sub get_percentage_exon_conversation_in_exon_cluster {
  my ( $self ) = @_ ;

  my @ex_clust = @{ $self->cluster->get_all_Exons_in_ExonCluster } ;

  # uniquify exon acc. to their hashkey 
  my %uniq_exons ;
  for (@ex_clust) {
    unless ($_->is_terminal_exon) {
      $uniq_exons { $_->hashkey }++ ;
    }
  }

  # get maximum value (most consered boundaries) out of hash
  my @tmp = reverse sort (values %uniq_exons ) ;

  my $max_cons = -1;
  if (scalar(@tmp) > 0) {
    $max_cons = shift @tmp ;
  }

  my $percentage_exon_conservation = 0 ;
  if  ($max_cons > 0  ) {
    if ($uniq_exons{$self->hashkey} ){
     $percentage_exon_conservation = $uniq_exons{$self->hashkey} / $max_cons ;
    }
  } else {
   $percentage_exon_conservation = 0 ;
  }
  return $percentage_exon_conservation ;
}
is_3prim_exondescriptionprevnextTop
sub is_3prim_exon {
  my ($self) = @_;
  return 1 if ($self->prev_exon && !$self->next_exon) ; 
  return 0 ;
}
is_5prim_exondescriptionprevnextTop
sub is_5prim_exon {
  my ($self) = @_;
  return 1 if ($self->next_exon && !$self->prev_exon) ; 
  return 0 ;
}
is_terminal_exondescriptionprevnextTop
sub is_terminal_exon {
  my ($self) = @_;
  if ($self->next_exon && $self->prev_exon) {
    return 0 ;
  }
  return  1 ;
}
newdescriptionprevnextTop
sub new {
  my($class) = shift;
  if( ref $class ) {
      $class = ref $class;
  }
  my $self = $class->SUPER::new(@_);
  return $self ;
}
next_exondescriptionprevnextTop
sub next_exon {
  my ($self,$value) = @_;
  if (defined($value)) {
    $self->{'next_exon'} = $value;
  }
  return $self->{'next_exon'};
}
number_exonsdescriptionprevnextTop
sub number_exons {
 my ($self) = @_ ; 
  if (defined($self->transcript)){ 
    return scalar( @{ $self->transcript->get_all_Exons} ) ; 
  }else {
    warning("Exon has no Bio::EnsEMBL::Transript-object attached - can't get number of exons\n" ) ; 
  }
  return undef ;
}
prev_exondescriptionprevnextTop
sub prev_exon {
  my ($self,$value) = @_;
  if (defined($value)) {
    $self->{'prev_exon'} = $value;
  }
  return $self->{'prev_exon'};
}
transcriptdescriptionprevnextTop
sub transcript {
  my ($self,$value) = @_;
  if (defined($value)) {
    $self->{'transcript'} = $value;
  }
  return $self->{'transcript'};
}
visiteddescriptionprevnextTop
sub visited {
  my ($self,$value) = @_;
  if (defined($value)) {
    $self->{'visited'} = $value;
  }
  return $self->{'visited'};
}
General documentation
SYNOPSIS (1)Top
  Creation by re-blessing:

  for my $t ( @transcripts ) { 
    bless $t,"Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::ExonExtended";

    $t->ev_set('est') ; 
  }  

  Creation without re-blessing : 

  my $tran = new Bio::EnsEMBL::Transcript(-EXONS => \@exons);
SYNOPSIS (2)Top
  Creation by re-blessing:

  for my $t ( @transcripts ) { 
    bless $t,"Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::ExonExtended";
    $t->ev_set('est') ; 
  }  

  Creation without re-blessing : 

  my $exon= new Bio::EnsEMBL::Exon(
                                  -START  =>   100 , 
                                  -END    =>   300,
                                  -STRAND => '-1', 
                                  -SLICE  => $slice,
                                  -ANALYSIS => $analysis, 
                                  );
CONTACTTop
Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
Top
   Name       : number_exons 
   Arg        : int
   Func       : getter/setter number of exons in Transcript
   Returntype : int