[stability-pipeline] update tests

KULL-Centre · Jul 27, 2022 · 522434d · 522434d
1 parent 2e0a8f7
commit 522434d
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Showing 9 changed files with 63 additions and 63 deletions.
diff --git a/...est/mp-pipeline/output/MPpipelineCreateGlpGTestCase_deepTMHMM/ddG/input/parse_ddgs.sbatch b/...est/mp-pipeline/output/MPpipelineCreateGlpGTestCase_deepTMHMM/ddG/input/parse_ddgs.sbatch
@@ -2,8 +2,8 @@
 #SBATCH --job-name=6xro_final_renum_p-ddg
 #SBATCH --array=1 
 #SBATCH --nodes=1 
-#SBATCH --time=0:10:00 
+#SBATCH --time=10:00:00 
 #SBATCH --partition=sbinlab 
 
 #This sbatch script launches the parse parse_rosetta_ddgs function, from the parse_cartesian_ddgs 
-python3XXXtagvXXX1
+python3 /parser_ddg_v2.py 6xro_final_renum A ERAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMANGAHIAGLAVGLAMAFVDSLNA /ddG/run /ddG/output /prepare/checking/structure_input.json /ddG/input /output /prepare/checking False True XXXtagvXXX /prepare/cleaning True 1
diff --git a/...est/mp-pipeline/output/MPpipelineCreateGlpGTestCase_homodimer/ddG/input/parse_ddgs.sbatch b/...est/mp-pipeline/output/MPpipelineCreateGlpGTestCase_homodimer/ddG/input/parse_ddgs.sbatch
@@ -2,8 +2,8 @@
 #SBATCH --job-name=homodimer-1afo_renum_uniquechain_p-ddg
 #SBATCH --array=1 
 #SBATCH --nodes=1 
-#SBATCH --time=0:10:00 
+#SBATCH --time=10:00:00 
 #SBATCH --partition=sbinlab 
 
 #This sbatch script launches the parse parse_rosetta_ddgs function, from the parse_cartesian_ddgs 
-python3XXXtagvXXX1
+python3 /parser_ddg_v2.py homodimer-1afo_renum_uniquechain A VQLAHHFSEPEITLIIFGVMAGVIGTILLISYGIRRLIKKVQLAHHFSEPEITLIIFGVMAGVIGTILLISYGIRRLIKK /ddG/run /ddG/output /prepare/checking/structure_input.json /ddG/input /output /prepare/checking False True XXXtagvXXX /prepare/cleaning True 1
diff --git a/...a/test/mp-pipeline/output/MPpipelineCreateGlpGTestCase_mutdir/ddG/input/parse_ddgs.sbatch b/...a/test/mp-pipeline/output/MPpipelineCreateGlpGTestCase_mutdir/ddG/input/parse_ddgs.sbatch
@@ -2,8 +2,8 @@
 #SBATCH --job-name=6xro_final_renum_p-ddg
 #SBATCH --array=1 
 #SBATCH --nodes=1 
-#SBATCH --time=0:10:00 
+#SBATCH --time=10:00:00 
 #SBATCH --partition=sbinlab 
 
 #This sbatch script launches the parse parse_rosetta_ddgs function, from the parse_cartesian_ddgs 
-python3XXXtagvXXX1
+python3 /parser_ddg_v2.py 6xro_final_renum A ERAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMANGAHIAGLAVGLAMAFVDSLNA /ddG/run /ddG/output /prepare/checking/structure_input.json /ddG/input /output /prepare/checking False True XXXtagvXXX /prepare/cleaning True 1
diff --git a/...t/mp-pipeline/output/MPpipelineCreateGlpGTestCase_pipemutfile/ddG/input/parse_ddgs.sbatch b/...t/mp-pipeline/output/MPpipelineCreateGlpGTestCase_pipemutfile/ddG/input/parse_ddgs.sbatch
@@ -2,8 +2,8 @@
 #SBATCH --job-name=6xro_final_renum_p-ddg
 #SBATCH --array=1 
 #SBATCH --nodes=1 
-#SBATCH --time=0:10:00 
+#SBATCH --time=10:00:00 
 #SBATCH --partition=sbinlab 
 
 #This sbatch script launches the parse parse_rosetta_ddgs function, from the parse_cartesian_ddgs 
-python3XXXtagvXXX1
+python3 /parser_ddg_v2.py 6xro_final_renum A ERAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMANGAHIAGLAVGLAMAFVDSLNA /ddG/run /ddG/output /prepare/checking/structure_input.json /ddG/input /output /prepare/checking False True XXXtagvXXX /prepare/cleaning True 1
diff --git a/...p-pipeline/output/MPpipelineCreateGlpGTestCase_rosettamutfile/ddG/input/parse_ddgs.sbatch b/...p-pipeline/output/MPpipelineCreateGlpGTestCase_rosettamutfile/ddG/input/parse_ddgs.sbatch
@@ -2,8 +2,8 @@
 #SBATCH --job-name=6xro_final_renum_p-ddg
 #SBATCH --array=1 
 #SBATCH --nodes=1 
-#SBATCH --time=0:10:00 
+#SBATCH --time=10:00:00 
 #SBATCH --partition=sbinlab 
 
 #This sbatch script launches the parse parse_rosetta_ddgs function, from the parse_cartesian_ddgs 
-python3XXXtagvXXX1
+python3 /parser_ddg_v2.py 6xro_final_renum A ERAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMANGAHIAGLAVGLAMAFVDSLNA /ddG/run /ddG/output /prepare/checking/structure_input.json /ddG/input /output /prepare/checking False True XXXtagvXXX /prepare/cleaning True 1
diff --git a/...a/test/sp-pipeline/output/SPpipelineCreateDHFRTestCase_ligand/ddG/input/parse_ddgs.sbatch b/...a/test/sp-pipeline/output/SPpipelineCreateDHFRTestCase_ligand/ddG/input/parse_ddgs.sbatch
@@ -2,8 +2,8 @@
 #SBATCH --job-name=4M6J_p-ddg
 #SBATCH --array=1 
 #SBATCH --nodes=1 
-#SBATCH --time=0:10:00 
+#SBATCH --time=10:00:00 
 #SBATCH --partition=sbinlab 
 
 #This sbatch script launches the parse parse_rosetta_ddgs function, from the parse_cartesian_ddgs 
-python3XXXtagvXXX2.9
+python3 /parser_ddg_v2.py 4M6J A SLNCIVAVSQNMGIGKNGDLPWPPLRNEFRYFQRMTTTSSVEGKQNLVIMGKKTWFSIPEKNRPLKGRINLVLSRELKEPPQGAHFLSRSLDDALKLTEQPELANKVDMVWIVGGSSVYKEAMNHPGHLKLFVTRIMQDFESDTFFPEIDLEKYKLLPEYPGVLSDVQEEKGIKYKFEVYEKND /ddG/run /ddG/output /prepare/checking/structure_input.json /ddG/input /output /prepare/checking False True XXXtagvXXX /prepare/cleaning False 2.9
diff --git a/...p-pipeline/output/SPpipelineCreateDHFRTestCase_rosettamutfile/ddG/input/parse_ddgs.sbatch b/...p-pipeline/output/SPpipelineCreateDHFRTestCase_rosettamutfile/ddG/input/parse_ddgs.sbatch
@@ -2,8 +2,8 @@
 #SBATCH --job-name=4M6J_p-ddg
 #SBATCH --array=1 
 #SBATCH --nodes=1 
-#SBATCH --time=0:10:00 
+#SBATCH --time=10:00:00 
 #SBATCH --partition=sbinlab 
 
 #This sbatch script launches the parse parse_rosetta_ddgs function, from the parse_cartesian_ddgs 
-python3XXXtagvXXX2.9
+python3 /parser_ddg_v2.py 4M6J A SLNCIVAVSQNMGIGKNGDLPWPPLRNEFRYFQRMTTTSSVEGKQNLVIMGKKTWFSIPEKNRPLKGRINLVLSRELKEPPQGAHFLSRSLDDALKLTEQPELANKVDMVWIVGGSSVYKEAMNHPGHLKLFVTRIMQDFESDTFFPEIDLEKYKLLPEYPGVLSDVQEEKGIKYKFEVYEKND /ddG/run /ddG/output /prepare/checking/structure_input.json /ddG/input /output /prepare/checking False True XXXtagvXXX /prepare/cleaning False 2.9
diff --git a/software/rosetta_ddG_pipeline/test/test_mp_pipeline.py b/software/rosetta_ddG_pipeline/test/test_mp_pipeline.py
@@ -57,7 +57,7 @@ def clean_reference_from_local_path(dir_name, local_path):
                     fp.write(s)
 
 
-def clean_version(dir_name, new_val='XXXtagvXXX', old_val=' .*tagv.* '):
+def clean_version(dir_name, new_val=' XXXtagvXXX ', old_val=r'\s?.\S+tagv.*?\s'):
     for dname, dirs, files in os.walk(dir_name):
         for fname in files:
             if (not fname.startswith('.')) and (not fname.endswith('.png')):
@@ -164,9 +164,9 @@ def test_create_rosettamutfile_prov_flag(self):
         ]
 
         today = date.today()
-        clean_version(self.output_dir, new_val='XXXtagvXXX')
+        clean_version(self.output_dir)
         clean_version(self.output_dir, new_val='', old_val=today.strftime("%d-%b-%y").upper())
-        clean_version(self.output_dir, new_val='\n', old_val='VERSION.*\n')
+        clean_version(self.output_dir, new_val='\n', old_val=r'VERSION.*\n')
         output_dic = {}
         for r, d, f in os.walk(self.output_dir):
             for file in f:
@@ -195,11 +195,11 @@ def test_create_rosettamutfile_prov_flag(self):
                      rosetta_paths.Rosetta_database_path, rosetta_paths.Rosetta_extension]
         clean_reference_from_local_path(
             self.reference_dir, elem)
-        clean_version(self.reference_dir, new_val='XXXtagvXXX')
-        clean_version(self.reference_dir, new_val='\n', old_val='HEADER .*\n')
-        clean_version(self.reference_dir, new_val='\n', old_val='REMARK .*\n')
+        clean_version(self.reference_dir)
+        clean_version(self.reference_dir, new_val='\n', old_val=r'HEADER .*\n')
+        clean_version(self.reference_dir, new_val='\n', old_val=r'REMARK .*\n')
         clean_version(self.reference_dir, new_val='', old_val=today.strftime("%d-%b-%y").upper())
-        clean_version(self.reference_dir, new_val='\n', old_val='VERSION.*\n')
+        clean_version(self.reference_dir, new_val='\n', old_val=r'VERSION.*\n')
 
         for r, d, f in os.walk(self.reference_dir):
             for file in f:
@@ -217,10 +217,10 @@ def test_create_rosettamutfile_prov_flag(self):
                             reference_dic[os.path.join(
                                 parent_directory, file)] = fp.read()
         self.maxDiff = None
-        print('test_create_rosettamutfile_prov_flag')
-        for key in output_dic.keys():
-            if output_dic[key]!=reference_dic[key]:
-                print(key)
+        # print('test_create_rosettamutfile_prov_flag')
+        # for key in output_dic.keys():
+        #     if output_dic[key]!=reference_dic[key]:
+        #         print(key)
         self.assertDictEqual(output_dic, reference_dic)
 
 
@@ -292,9 +292,9 @@ def test_create_pipemut_prov_flag(self):
         ]
 
         today = date.today()
-        clean_version(self.output_dir, new_val='XXXtagvXXX')
+        clean_version(self.output_dir)
         clean_version(self.output_dir, new_val='', old_val=today.strftime("%d-%b-%y").upper())
-        clean_version(self.output_dir, new_val='\n', old_val='VERSION.*\n')
+        clean_version(self.output_dir, new_val='\n', old_val=r'VERSION.*\n')
         output_dic = {}
         for r, d, f in os.walk(self.output_dir):
             for file in f:
@@ -323,9 +323,9 @@ def test_create_pipemut_prov_flag(self):
                      rosetta_paths.Rosetta_database_path, rosetta_paths.Rosetta_extension]
         clean_reference_from_local_path(
             self.reference_dir, elem)
-        clean_version(self.reference_dir, new_val='XXXtagvXXX')
+        clean_version(self.reference_dir)
         clean_version(self.reference_dir, new_val='', old_val=today.strftime("%d-%b-%y").upper())
-        clean_version(self.reference_dir, new_val='\n', old_val='VERSION.*\n')
+        clean_version(self.reference_dir, new_val='\n', old_val=r'VERSION.*\n')
         for r, d, f in os.walk(self.reference_dir):
             for file in f:
                 file_join = os.path.join(r, file)
@@ -342,10 +342,10 @@ def test_create_pipemut_prov_flag(self):
                             reference_dic[os.path.join(
                                 parent_directory, file)] = fp.read()
         self.maxDiff = None
-        print('test_create_pipemut_prov_flag')
-        for key in output_dic.keys():
-            if output_dic[key]!=reference_dic[key]:
-                print(key)
+        # print('test_create_pipemut_prov_flag')
+        # for key in output_dic.keys():
+        #     if output_dic[key]!=reference_dic[key]:
+        #         print(key)
         self.assertDictEqual(output_dic, reference_dic)
 
 
@@ -419,9 +419,9 @@ def test_create_mutdir_prov_flag(self):
         ]
 
         today = date.today()
-        clean_version(self.output_dir, new_val='XXXtagvXXX')
+        clean_version(self.output_dir)
         clean_version(self.output_dir, new_val='', old_val=today.strftime("%d-%b-%y").upper())
-        clean_version(self.output_dir, new_val='\n', old_val='VERSION.*\n')
+        clean_version(self.output_dir, new_val='\n', old_val=r'VERSION.*\n')
         output_dic = {}
         for r, d, f in os.walk(self.output_dir):
             for file in f:
@@ -450,9 +450,9 @@ def test_create_mutdir_prov_flag(self):
                      rosetta_paths.Rosetta_database_path, rosetta_paths.Rosetta_extension]
         clean_reference_from_local_path(
             self.reference_dir, elem)
-        clean_version(self.reference_dir, new_val='XXXtagvXXX')
+        clean_version(self.reference_dir)
         clean_version(self.reference_dir, new_val='', old_val=today.strftime("%d-%b-%y").upper())
-        clean_version(self.reference_dir, new_val='\n', old_val='VERSION.*\n')
+        clean_version(self.reference_dir, new_val='\n', old_val=r'VERSION.*\n')
         for r, d, f in os.walk(self.reference_dir):
             for file in f:
                 file_join = os.path.join(r, file)
@@ -469,10 +469,10 @@ def test_create_mutdir_prov_flag(self):
                             reference_dic[os.path.join(
                                 parent_directory, file)] = fp.read()
         self.maxDiff = None
-        print('test_create_mutdir_prov_flag')
-        for key in output_dic.keys():
-            if output_dic[key]!=reference_dic[key]:
-                print(key)
+        # print('test_create_mutdir_prov_flag')
+        # for key in output_dic.keys():
+        #     if output_dic[key]!=reference_dic[key]:
+        #         print(key)
         self.assertDictEqual(output_dic, reference_dic)
 
 
@@ -544,9 +544,9 @@ def test_create_homodimer_prov_flag(self):
             'input_mp_aligned_atm',
         ]
         today = date.today()
-        clean_version(self.output_dir, new_val='XXXtagvXXX')
+        clean_version(self.output_dir)
         clean_version(self.output_dir, new_val='', old_val=today.strftime("%d-%b-%y").upper())
-        clean_version(self.output_dir, new_val='\n', old_val='VERSION.*\n')
+        clean_version(self.output_dir, new_val='\n', old_val=r'VERSION.*\n')
         output_dic = {}
         for r, d, f in os.walk(self.output_dir):
             for file in f:
@@ -575,9 +575,9 @@ def test_create_homodimer_prov_flag(self):
                      rosetta_paths.Rosetta_database_path, rosetta_paths.Rosetta_extension]
         clean_reference_from_local_path(
             self.reference_dir, elem)
-        clean_version(self.reference_dir, new_val='XXXtagvXXX')
+        clean_version(self.reference_dir)
         clean_version(self.reference_dir, new_val='', old_val=today.strftime("%d-%b-%y").upper())
-        clean_version(self.reference_dir, new_val='\n', old_val='VERSION.*\n')
+        clean_version(self.reference_dir, new_val='\n', old_val=r'VERSION.*\n')
         for r, d, f in os.walk(self.reference_dir):
             for file in f:
                 file_join = os.path.join(r, file)
@@ -594,10 +594,10 @@ def test_create_homodimer_prov_flag(self):
                             reference_dic[os.path.join(
                                 parent_directory, file)] = fp.read()
         self.maxDiff = None
-        print('test_create_homodimer_prov_flag')
-        for key in output_dic.keys():
-            if output_dic[key]!=reference_dic[key]:
-                print(key)
+        # print('test_create_homodimer_prov_flag')
+        # for key in output_dic.keys():
+        #     if output_dic[key]!=reference_dic[key]:
+        #         print(key)
         self.assertDictEqual(output_dic, reference_dic)
 
 
@@ -618,7 +618,7 @@ def test_create_deepTMHMM_prov_flag(self):
             'RUN_STRUC': None,
             'LIGAND': None,
             'OVERWRITE_PATH': True,
-            'SLURM_PARTITION': 'sbinlab_ib',
+            'SLURM_PARTITION': 'sbinlab',
             'GAPS_OUTPUT': False,
             'DUMP_PDB': 0,
             'DO_CHECKING': True,
@@ -664,9 +664,9 @@ def test_create_deepTMHMM_prov_flag(self):
             'mutation_clean.txt', 
         ]
         today = date.today()
-        clean_version(self.output_dir, new_val='XXXtagvXXX')
+        clean_version(self.output_dir)
         clean_version(self.output_dir, new_val='', old_val=today.strftime("%d-%b-%y").upper())
-        clean_version(self.output_dir, new_val='\n', old_val='VERSION.*\n')
+        clean_version(self.output_dir, new_val='\n', old_val=r'VERSION.*\n')
         output_dic = {}
         for r, d, f in os.walk(self.output_dir):
             for file in f:
@@ -694,9 +694,9 @@ def test_create_deepTMHMM_prov_flag(self):
                      rosetta_paths.Rosetta_main_path, rosetta_paths.Rosetta_tools_path,
                      rosetta_paths.Rosetta_database_path, rosetta_paths.Rosetta_extension]
         clean_reference_from_local_path(self.reference_dir, elem)
-        clean_version(self.reference_dir, new_val='XXXtagvXXX')
+        clean_version(self.reference_dir)
         clean_version(self.reference_dir, new_val='', old_val=today.strftime("%d-%b-%y").upper())
-        clean_version(self.reference_dir, new_val='\n', old_val='VERSION.*\n')
+        clean_version(self.reference_dir, new_val='\n', old_val=r'VERSION.*\n')
         for r, d, f in os.walk(self.reference_dir):
             for file in f:
                 file_join = os.path.join(r, file)
@@ -713,9 +713,9 @@ def test_create_deepTMHMM_prov_flag(self):
                             reference_dic[os.path.join(
                                 parent_directory, file)] = fp.read()
         self.maxDiff = None
-        print('test_create_deepTMHMM_prov_flag')
-        for key in output_dic.keys():
-            if output_dic[key]!=reference_dic[key]:
-                print(key)
+        # print('test_create_deepTMHMM_prov_flag')
+        # for key in output_dic.keys():
+        #     if output_dic[key]!=reference_dic[key]:
+        #         print(key)
         self.assertDictEqual(output_dic, reference_dic)
 
diff --git a/software/rosetta_ddG_pipeline/test/test_sp_pipeline.py b/software/rosetta_ddG_pipeline/test/test_sp_pipeline.py
@@ -57,7 +57,7 @@ def clean_reference_from_local_path(dir_name, local_path):
                     fp.write(s)
 
 
-def clean_version(dir_name, new_val='XXXtagvXXX', old_val=' .*tagv.* '):
+def clean_version(dir_name, new_val=' XXXtagvXXX ', old_val=r'\s?.\S+tagv.*?\s'):
     for dname, dirs, files in os.walk(dir_name):
         for fname in files:
             if not fname.startswith('.'):
@@ -157,7 +157,7 @@ def test_create_rosettamutfile_prov_flag(self):
         ]
 
         today = date.today()
-        clean_version(self.output_dir, new_val='XXXtagvXXX')
+        clean_version(self.output_dir)
         clean_version(self.output_dir, new_val='', old_val=today.strftime("%d-%b-%y").upper())
         output_dic = {}
         for r, d, f in os.walk(self.output_dir):
@@ -187,7 +187,7 @@ def test_create_rosettamutfile_prov_flag(self):
                      rosetta_paths.Rosetta_database_path, rosetta_paths.Rosetta_extension]
         clean_reference_from_local_path(
             self.reference_dir, elem)
-        clean_version(self.reference_dir, new_val='XXXtagvXXX')
+        clean_version(self.reference_dir)
         clean_version(self.reference_dir, new_val='', old_val=today.strftime("%d-%b-%y").upper())
 
         for r, d, f in os.walk(self.reference_dir):
@@ -275,7 +275,7 @@ def test_create_ligand_prov_flag(self):
         ]
 
         today = date.today()
-        clean_version(self.output_dir, new_val='XXXtagvXXX')
+        clean_version(self.output_dir)
         clean_version(self.output_dir, new_val='', old_val=today.strftime("%d-%b-%y").upper())
         output_dic = {}
         for r, d, f in os.walk(self.output_dir):
@@ -305,7 +305,7 @@ def test_create_ligand_prov_flag(self):
                      rosetta_paths.Rosetta_database_path, rosetta_paths.Rosetta_extension]
         clean_reference_from_local_path(
             self.reference_dir, elem)
-        clean_version(self.reference_dir, new_val='XXXtagvXXX')
+        clean_version(self.reference_dir)
         clean_version(self.reference_dir, new_val='\n', old_val=today.strftime("%d-%b-%y").upper())
 
         for r, d, f in os.walk(self.reference_dir):