Module: ViennaRna::Global::RunExtensions::InstanceMethods
- Defined in:
- lib/vienna_rna/global/run_extensions.rb
Instance Method Summary collapse
- #base_flags(flags) ⇒ Object
- #exec_name ⇒ Object
- #pre_run_check ⇒ Object
- #recursively_merge_flags(flags) ⇒ Object
- #run(flags = {}) ⇒ Object
- #run_command(flags) ⇒ Object
- #stringify_flags(flags) ⇒ Object
Instance Method Details
#base_flags(flags) ⇒ Object
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# File 'lib/vienna_rna/global/run_extensions.rb', line 66 def base_flags(flags) default_flags.respond_to?(:call) ? default_flags[self, flags] : default_flags end |
#exec_name ⇒ Object
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# File 'lib/vienna_rna/global/run_extensions.rb', line 48 def exec_name executable_name.respond_to?(:call) ? executable_name[self] : executable_name end |
#pre_run_check ⇒ Object
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# File 'lib/vienna_rna/global/run_extensions.rb', line 42 def pre_run_check if %x[which #{exec_name}].empty? raise RuntimeError.new("#{exec_name} is not defined on this machine") end end |
#recursively_merge_flags(flags) ⇒ Object
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# File 'lib/vienna_rna/global/run_extensions.rb', line 52 def recursively_merge_flags(flags) rmerge = ->(old_hash, new_hash) do inner_hash = {} old_hash.merge(new_hash) do |key, old_value, new_value| inner_hash[key] = [old_value, new_value].map(&:class).uniq == [Hash] ? rmerge[old_value, new_value] : new_value end end rmerge[base_flags(flags), flags].tap do |merged_flags| ViennaRna.debugger { "%s: %s" % [self.class.name, merged_flags.inspect] } end end |
#run(flags = {}) ⇒ Object
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# File 'lib/vienna_rna/global/run_extensions.rb', line 21 def run(flags = {}) unless @response tap do @runtime = Benchmark.measure do pre_run_check merged_flags = recursively_merge_flags(flags) runnable_command = run_command(merged_flags) ViennaRna.debugger { runnable_command } @response = %x[#{runnable_command}] post_process if respond_to?(:post_process) end ViennaRna.debugger { "Total runtime: %.3f sec." % runtime.real } end else self end end |
#run_command(flags) ⇒ Object
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# File 'lib/vienna_rna/global/run_extensions.rb', line 70 def run_command(flags) "echo %s | %s %s" % [ "'%s'" % call_with.map { |datum| data.send(datum) }.join(?\n), exec_name, stringify_flags(flags) ] end |
#stringify_flags(flags) ⇒ Object
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# File 'lib/vienna_rna/global/run_extensions.rb', line 78 def stringify_flags(flags) flags.inject("") do |string, (flag, value)| (string + (value == :empty ? " -%s" % flag : " -%s %s" % [flag, value])).strip end end |