renammed modules

dna_add.sh

@@ -133,7 +133,7 @@ fi
 
 #----Homopolymere Deletion----#
 
-#h_deletion_script="$project_dir"/synthesis_simulation/homoplymere_deletion/homopolymere_deletion.py
+#h_deletion_script="$project_dir"/synthesis_modules/homoplymere_deletion/homopolymere_deletion.py
 fragments_path="$stored_document_path"/3_final_fragments.fasta
 
 echo "homopolymere deletion not implemented yet; skipping..."

dna_store.sh

@@ -128,7 +128,7 @@ fi
 #copy all the fragments from all the documents into one file
 cat "$container_path"/*/3_final_fragments.fasta > "$container_path"/container_fragments.fasta
 
-primers_generation_script="$project_dir"/synthesis_simulation/primer_generation.py
+primers_generation_script="$project_dir"/synthesis_modules/primer_generation.py
 
 call_function python3 "$primers_generation_script" -c "$container_path"
 
@@ -139,7 +139,7 @@ simulation=$(get_container_param $container_path "simulation")
 
 if [ $simulation ]
 then
-	synthesis_script="$project_dir"/synthesis_simulation/fragment_synthesis.py
+	synthesis_script="$project_dir"/synthesis_modules/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
@@ -155,7 +155,7 @@ fi
 
 if [ $simulation ]
 then
-	molecule_design_script="$project_dir"/synthesis_simulation/fragment_assembly.py
+	molecule_design_script="$project_dir"/synthesis_modules/fragment_assembly.py
 	
 	assembly_type=$(get_container_param $container_path "assembly_type")
 	spacer=$(get_container_param $container_path "spacer")