Bio::EnsEMBL::Analysis::RunnableDB BlastRfam
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Summary
  Bio::EnsEMBL::Analysis::RunnableDB::BlastRfam
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Analysis::Config::Blast
Bio::EnsEMBL::Analysis::Config::Databases qw ( DATABASES DNA_DBNAME )
Bio::EnsEMBL::Analysis::Config::General
Bio::EnsEMBL::Analysis::Runnable::BlastRfam
Bio::EnsEMBL::Analysis::RunnableDB::BaseGeneBuild
Bio::EnsEMBL::Analysis::RunnableDB::Blast
Bio::EnsEMBL::Utils::Exception qw ( throw warning )
Inherit
Bio::EnsEMBL::Analysis::RunnableDB::BaseGeneBuild Bio::EnsEMBL::Analysis::RunnableDB::Blast
Synopsis
  my $blast = Bio::EnsEMBL::Analysis::RunnableDB::BlastRfam->
  new(
      -analysis => $analysis,
      -db => $db,
      -input_id => 'contig::AL1347153.1.3517:1:3571:1'
     );
  $blast->fetch_input;
  $blast->run;
  my @output =@{$blast->output};
Description
Modified blast runnable for specific use with RFAMSEQ.
Use for running BLASTN of genomic vs RFAMSEQ prior to
ncRNA analysis using Infernal.
Slice size seems best around 200k
Methods
fetch_inputDescriptionCode
Methods description
fetch_inputcode    nextTop
  Arg [1]   : Bio::EnsEMBL::Analysis::RunnableDB::Blast
  Function  : fetch sequence out of database, instantiate the filter, 
  parser and finally the blast runnable
  Returntype: 1
  Exceptions: none
  Example   :
Methods code
fetch_inputdescriptionprevnextTop
sub fetch_input {
  my ($self) = @_; 
 
  # attach dna-db to db
  my $dna_db = $self->get_dbadaptor($DNA_DBNAME); 
  $self->db->dnadb($dna_db); 

  my $slice = $self->fetch_sequence($self->input_id, $self->db,['Dust']);
  $self->query($slice);
  my %blast = %{$self->BLAST_PARAMS};
   my $parser = $self->make_parser;
  my $filter;
  if($self->BLAST_FILTER){
    $filter = $self->make_filter;
  }
  my $seq = $self->query;
  my $runnable = Bio::EnsEMBL::Analysis::Runnable::BlastRfam->new
    (
     -query    => $seq,
     -program  => $self->analysis->program_file,
     -parser   => $parser,
     -filter   => $filter,
     -database => $self->analysis->db_file,
     -analysis => $self->analysis,
     -params   =>\% blast,
    );
  $self->runnable($runnable);
  return 1;
}
General documentation
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