fix buf removing some assemblies

eBlock_assembly_simulation.py

@@ -80,6 +80,10 @@ def assemble_blocks_simulation(eBlocks_list: list, nbr_mol: int) -> dict:
         for block in eBlocks_list[1:]:
             last_overhang = current_assembly[-overhang_size:]
             
+            if block[:overhang_size] != last_overhang:
+                print("error assembly simulation, overhangs not compatibles", last_overhang, block[-overhang_size:])
+                exit(1)
+            
             overhang_link_proba = float(overhang_assembly_stats_dict[last_overhang])
             
             if random.random() <= overhang_link_proba: # chance to succeed overhang linking
@@ -91,6 +95,7 @@ def assemble_blocks_simulation(eBlocks_list: list, nbr_mol: int) -> dict:
                 
         # add the assembly to the dict
         assembly_dict["molecule_"+str(mol_index)] = current_assembly
+        mol_index += 1
     
     return assembly_dict
 
@@ -146,7 +151,8 @@ def eBlocks_assembly(input_path: str, output_path: str, nbr_mol: int) -> None:
     # simulate bsaI digestion
     blocks_list = digest_bsaI(blocks_list)
     # simulation assembly by overhangs, fatal error if overhangs are not compatibles for successive blocks
-    assembly_dict = assemble_blocks(blocks_list)
+    #assembly_dict = assemble_blocks(blocks_list)
+    assembly_dict = assemble_blocks_simulation(blocks_list, nbr_mol)
     # save the assemblies into file
     dfr.save_dict_to_fasta(assembly_dict, output_path)
 
@@ -156,7 +162,7 @@ def container_assembly(input_dir_path, output_dir_path, nbr_mol):
     
     for filename in os.listdir(input_dir_path):
         file_path = os.path.join(input_dir_path, filename)
-
+        
         if os.path.isdir(file_path):
             input_file = file_path+"/5_blocks_buffer.fasta"
             output_file = os.path.join(output_dir_path, filename+".fasta")