bug fix

Synced with lutianyu2001/TIR-Learner at 2024-01-12 04:35 (CST)

bin/TIR-Learner3.0/TIR-Learner3.0.py

@@ -64,7 +64,8 @@
     GRF_path = parsed_args.grf_path.replace('"', "")
     gt_path = parsed_args.gt_path.replace('"', "")
     additional_args = prog_const.process_additional_args(parsed_args.additional_args.split(" "))
-    print(f"INFO: Additional args: {additional_args} accepted.")
+    if len(additional_args) != 0:
+        print(f"INFO: Additional args: {additional_args} accepted.")
 
     # Transforming the possible relative path into absolute path
     genome_file = os.path.abspath(genome_file)

bin/TIR-Learner3.0/bin/main.py

@@ -35,7 +35,7 @@ class TIRLearner:
     def __init__(self, genome_file_path: str, genome_name: str, species: str, TIR_length: int,
                  cpu_cores: int, GRF_mode: str,
                  working_dir_path: str, output_dir_path: str, checkpoint_dir_input_path: str,
-                 flag_verbose: bool, flag_debug: bool, GRF_path: str, gt_path: str, additional_args: list):
+                 flag_verbose: bool, flag_debug: bool, GRF_path: str, gt_path: str, additional_args: tuple):
         self.genome_file_path = genome_file_path
         self.genome_name = genome_name
         self.species = species
@@ -96,7 +96,7 @@ def clear(self):
         self.working_df_dict.clear()
 
     def execute(self):
-        self.mount_working_dir()
+        temp_dir = self.mount_working_dir()
         self.load_checkpoint_file()
         self.pre_scan_fasta_file()
         # print(os.getcwd())  # TODO ONLY FOR DEBUG REMOVE AFTER FINISHED
@@ -114,8 +114,12 @@ def execute(self):
         if prog_const.CHECKPOINT_OFF not in self.additional_args and not self.flag_debug:
             shutil.rmtree(self.checkpoint_dir_output_path)
 
-        subprocess.Popen(["unlink", self.genome_file_path]).wait()
-        os.rmdir(self.working_dir_path)
+        # subprocess.Popen(["unlink", self.genome_file_path]).wait()
+        # os.rmdir(self.working_dir_path)
+        if temp_dir is not None:
+            shutil.rmtree(temp_dir)
+        else:
+            shutil.rmtree(self.working_dir_path)
 
     def pre_scan_fasta_file(self):
         # names = [record.id for record in SeqIO.parse(self.genome_file, "fasta")]
@@ -166,14 +170,17 @@ def pre_scan_fasta_file(self):
 
     def mount_working_dir(self):
         if self.working_dir_path is None:
-            self.working_dir_path = tempfile.mkdtemp()
+            temp_dir = tempfile.mkdtemp()
+            self.working_dir_path = temp_dir
         # self.load_genome_file()
         else:
+            temp_dir = None
             os.makedirs(self.working_dir_path, exist_ok=True)
         self.working_dir_path = os.path.join(self.working_dir_path, prog_const.sandbox_dir_name)
         os.makedirs(self.working_dir_path, exist_ok=True)
         self.working_dir_path = os.path.abspath(self.working_dir_path)
         os.chdir(self.working_dir_path)
+        return temp_dir
 
     # def load_genome_file(self):
     #     genome_file_soft_link = os.path.join(self.execution_dir, "genome_file_soft_link.fa.lnk")

bin/TIR-Learner3.0/bin/prog_const.py

@@ -30,8 +30,9 @@
 mix_short_seq_process_num = 2
 
 
-def process_additional_args(additional_args: list) -> list:
-    processed_additional_args = list(map(additional_args_mapping_dict.get, additional_args))
+def process_additional_args(additional_args: list) -> tuple:
+    processed_additional_args = tuple(i for i in
+                                      tuple(map(additional_args_mapping_dict.get, additional_args)) if i is not None)
     if SKIP_TIRVISH in processed_additional_args and SKIP_GRF in processed_additional_args:
         raise SystemExit("ERROR: \"skip_tirvish\" and \"skip_grf\" cannot be specified at the same time!")
     return processed_additional_args

bin/TIR-Learner3.0/bin/run_GRF.py

@@ -181,9 +181,10 @@ def cpu_cores_allocation_GRF_boost(cpu_cores, job_bound_type="cpu_bound"):
         num_threads_total = cpu_cores
 
     num_processes = int(math.sqrt(num_threads_total))
-    num_threads_per_process = int(num_threads_total / num_processes)
-    num_extra_threads = num_threads_per_process - num_processes * num_threads_per_process
-    num_extra_threads = 0 if num_extra_threads < 0 else num_extra_threads
+    num_threads_per_process = int(num_threads_total / num_processes) * 4
+    # num_extra_threads = num_threads_per_process - num_processes * num_threads_per_process
+    # num_extra_threads = 0 if num_extra_threads < 0 else num_extra_threads
+    num_extra_threads = 0
     return num_processes, num_threads_per_process, num_extra_threads
 
 
@@ -231,7 +232,7 @@ def execute(TIRLearner_instance):
     # for i in os.listdir(os.getcwd()):
     #     shutil.copyfile(os.path.join(os.getcwd(), i), os.path.join(TIRLearner_instance.output_dir, i))
 
-    print()
+    print("  Step 1/2: Executing GRF\n")
     if GRF_mode == "mix":
         run_GRF_mix(records_split_file_name, filtered_genome_file_name, GRF_path, cpu_cores, TIR_length)
     elif GRF_mode == "boost":
@@ -240,4 +241,5 @@ def execute(TIRLearner_instance):
         run_GRF_native(filtered_genome_file_name, GRF_path, cpu_cores, TIR_length)
     print()
 
+    print("  Step 2/2: Getting GRF result")
     return get_GRF_result_df(GRF_result_dir_name)

bin/TIR-Learner3.0/bin/run_TIRvish.py

@@ -69,6 +69,8 @@ def execute(TIRLearner_instance):
     flag_verbose = TIRLearner_instance.flag_verbose
     gt_path = TIRLearner_instance.gt_path
 
+    print("  Step 1/2: Executing TIRvish")
     TIRvish_result_gff3_file_name = run_TIRvish(genome_file, genome_name, TIR_length, gt_path)
+    print("  Step 2/2: Getting TIRvish result")
     df = get_TIRvish_result_df(TIRvish_result_gff3_file_name)
     return get_fasta_pieces_SeqIO(genome_file, df, cpu_cores, flag_verbose)