+ FileUtils.cp orig_input, "#{hmm_name}/#{orig_input}"
+ end
+
+ 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}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
+ run_1 = true
+ FileUtils.cp "#{dsx_output}.fasta", "#{msa_dir}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
+ end
+
+ unless File.exist? "#{msa_100_dir}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
+ run_100 = true
+ FileUtils.cp "#{dsx_output}.fasta", "#{msa_100_dir}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
+ end
+
+ if File.exist?( TEMPLATE_FILE )
+ if run_1
+ FileUtils.cp TEMPLATE_FILE, msa_dir
+ end
+ if run_100
+ FileUtils.cp TEMPLATE_FILE, msa_100_dir
+ end
+
+ if LAUNCH_ANALYSIS && ( run_1 || run_100 )
+ puts "f. analysis:"
+ if run_1
+ Dir.chdir msa_dir
+ run_command "#{PF} -b=1 -s"
+ Dir.chdir "../.."
+ end
+ if run_100
+ Dir.chdir msa_100_dir
+ run_command "#{PF} -b=100 -s"
+ Dir.chdir "../.."
+ end
+ puts
+ end