refactor

dna_store.sh

@@ -139,7 +139,7 @@ simulation=$(get_container_param $container_path "simulation")
 
 if [ $simulation ]
 then
-	synthesis_script="$project_dir"/synthesis_simulation/synthesis.py
+	synthesis_script="$project_dir"/synthesis_simulation/fragment_synthesis.py
 	
 	for directory in "$container_path"/*/ ; do
 		call_function python3 "$synthesis_script" -i "$directory"/3_final_fragments.fasta -o "$directory"/4_synthesis.fasta -n $n_synth --i_error $i_error --d_error $d_error --s_error $s_error
@@ -151,11 +151,11 @@ else
 fi
 
 
-#----Molecule design----#
+#----Fragment assembly----#
 
 if [ $simulation ]
 then
-	molecule_design_script="$project_dir"/synthesis_simulation/molecule_design.py
+	molecule_design_script="$project_dir"/synthesis_simulation/fragment_assembly.py
 	
 	assembly_type=$(get_container_param $container_path "assembly_type")
 	spacer=$(get_container_param $container_path "spacer")