remove primers generation, use fragment design instead, renamed outputs

dna_store.sh

@@ -123,15 +123,19 @@ then
 fi
 
 
-#----Primers Generation----#
+#----Fragments Design----#
 
 #copy all the fragments from all the documents into one file
-cat "$container_path"/*/3_final_fragments.fasta > "$container_path"/container_fragments.fasta
+#cat "$container_path"/*/3_final_fragments.fasta > "$container_path"/container_fragments.fasta
 
-primers_generation_script="$project_dir"/synthesis_modules/primer_generation.py
+# get the fragment length from the container options
+frag_length=$(get_container_param "$container_path" "frag_length")
 
-call_function python3 "$primers_generation_script" -c "$container_path"
+fragment_design_script="$project_dir"/synthesis_modules/ordered_fragment_design.py
 
+for directory in "$container_path"/*/ ; do
+	call_function python3 "$fragment_design_script" -i "$directory"/1_channel.fasta -o "$directory"/2_fragments.fasta -l $frag_length --cont_doc "$directory"
+done
 
 #----Synthesis----#
 
@@ -142,7 +146,7 @@ then
 	synthesis_script="$project_dir"/synthesis_modules/synthesis_simulation.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 $s_error
+		call_function python3 "$synthesis_script" -i "$directory"/2_fragments.fasta -o "$directory"/3_synthesis.fasta -n $n_synth --i_error $i_error --d_error $d_error --s_error $s_error
 	done
 else
 	echo "container is not in simulation mode"
@@ -158,19 +162,16 @@ then
 	molecule_design_script="$project_dir"/synthesis_modules/assembly_simulation.py
 	
 	assembly_type=$(get_container_param $container_path "assembly_type")
-	spacer=$(get_container_param $container_path "spacer")
 	
 	for directory in "$container_path"/*/ ; do
 		document_index=$(basename $directory)
 		n_frag=$(get_doc_param $container_path $document_index "fragment_number")
-		start_primer=$(get_doc_param $container_path $document_index "start_primer")
-		stop_primer=$(get_doc_param $container_path $document_index "stop_primer")
 		n_mol=$(($n_frag * 200)) #TODO
 				
-		call_function python3 "$molecule_design_script" -i "$directory"/4_synthesis.fasta -o "$directory"/5_molecules.fasta -t $assembly_type -s $spacer --start $start_primer --stop $stop_primer -n $n_mol
+		call_function python3 "$molecule_design_script" -i "$directory"/3_synthesis.fasta -o "$directory"/4_molecules.fasta -t $assembly_type -f $n_frag -n $n_mol
 	done
 	#concatenate all the molecules files into one to represent the physical container
-	cat "$container_path"/*/5_molecules.fasta > "$container_path"/container_molecules.fasta
+	cat "$container_path"/*/4_molecules.fasta > "$container_path"/container_molecules.fasta
 else
 	echo "container is not in simulation mode"
 	exit 0