- if File.exists?( TEMPLATE_FILE )
- FileUtils.cp TEMPLATE_FILE, "#{hmm_name}/msa/"
- FileUtils.cp TEMPLATE_FILE, "#{hmm_name}/msa100/"
+ 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