Class: RaxmlGammaSearch

Inherits:
Raxml
  • Object
show all
Includes:
TreeCheck
Defined in:
lib/rraxml.rb

Instance Attribute Summary

Attributes inherited from Raxml

#binary, #infofile, #name, #ops, #outdir, #phylip, #stderr, #stdout

Instance Method Summary collapse

Methods included from TreeCheck

#check_correctAlignment, #check_fulltree

Methods inherited from Raxml

#after_run, #before_run, #run, #salute

Constructor Details

#initialize(opts) ⇒ RaxmlGammaSearch

Returns a new instance of RaxmlGammaSearch.



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# File 'lib/rraxml.rb', line 172

def initialize(opts)
  super(opts)
  check_correctAlignment
  @num_trees = opts[:num_gamma_trees] 
  if opts[:num_threads].nil? 
    @binary = 'raxmlHPC-SSE3'
    @num_threads = 0
  else
    @binary = 'raxmlHPC-PTHREADS-SSE3'
    @num_threads = opts[:num_threads].to_i
  end
end

Instance Method Details

#complete_call ⇒ Object 



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# File 'lib/rraxml.rb', line 184

def complete_call
  @ops += " -m GTRCAT -p #{@seed} -N #{@num_trees}"
  @ops += " -T #{@num_threads} " if @num_threads > 0
end

#gather_outfiles ⇒ Object 



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# File 'lib/rraxml.rb', line 188

def gather_outfiles
  @outfiles += ["RAxML_bestTree.#{@name}"]
  other_files = ["result", "log", "parsimonyTree"]
  if @num_trees > 1
    @num_trees.times{|num| @outfiles += other_files.map{|n| "RAxML_" + n + ".#{@name}.RUN.#{num.to_s}"} }
  else
    @outfiles += other_files.map{|n| "RAxML_" + n + ".#{@name}"}
  end
end