Class: Mizlab::Blast

Inherits:
Bio::Blast
  • Object
show all
Defined in:
lib/mizlab.rb

Instance Method Summary collapse

Instance Method Details

#query(q, opts = {}) ⇒ Bio::Blast::Report

Execute blast+

Parameters:

  • q (Bio::Sequence, Bio::Sequence::NA, Bio::Sequence::AA) —

    Query sequence

  • opts (Hash) (defaults to: {}) —

    commandline arguments optionaly

Returns:

  • (Bio::Blast::Report) —

    Result for blast+



294
295
296
297
298
299
300
301
302
303
304
305
306
 
# File 'lib/mizlab.rb', line 294

def query(q, opts = {})
  # NOTE: I dont use **kwargs for compatibility
  case q
  when Bio::Sequence
    q = q.output(:fasta)
  when Bio::Sequence::NA, Bio::Sequence::AA, Bio::Sequence::Generic
    q = q.to_fasta("query", 70)
  else
    q = q.to_s
  end
  stdout, _ = exec_local(q, opts)
  return parse_result(stdout)
end