Bio::EnsEMBL::Analysis::RunnableDB BlastmiRNA
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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::BlastmiRNA
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::BlastmiRNA->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 miRNA
Use for running BLASTN of genomic sequence vs miRNAs prior to
miRNA anaysis
Slice size seems best around 200k
Methods
fetch_inputDescriptionCode
Methods description
fetch_inputcode    nextTop
  Arg [1]   : None
  Function  : fetch sequence out of database, instantiate the filter,
            : parser and finally the blast runnable
  Returntype: None
  Exceptions: none
  Example   : $blast->fetch_input;
Methods code
fetch_inputdescriptionprevnextTop
sub fetch_input {
  my ($self) = @_;  

  #add dna_db
  my $dna_db = $self->get_dbadaptor($DNA_DBNAME) ; 
  $self->db->dnadb($dna_db); 

  my $slice = $self->fetch_sequence($self->input_id, $self->db,'');
  $self->query($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::BlastmiRNA->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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