+ msa_dir = hmm_name + "/msa_ee#{e_value_exp.to_s}_#{length}"
+ msa_100_dir =hmm_name + "/msa100_ee#{e_value_exp.to_s}_#{length}"
+
+ unless File.exist? msa_dir
+ Dir.mkdir( msa_dir )
+ end
+ unless File.exist? msa_100_dir
+ Dir.mkdir( msa_100_dir )
+ end
+
+ run_1 = false
+ run_100 = false
+
+ unless File.exist? "#{msa_dir}/#{dsx_output}"
+ run_1 = true
+ FileUtils.cp "#{dsx_output}.fasta", "#{msa_dir}/#{dsx_output}"
+ end
+
+ unless File.exist? "#{msa_100_dir}/#{dsx_output}"
+ run_100 = true
+ FileUtils.cp "#{dsx_output}.fasta", "#{msa_100_dir}/#{dsx_output}"
+ end