geney 1.1.7__py2.py3-none-any.whl → 1.1.9__py2.py3-none-any.whl

geney/netchop.py

@@ -8,7 +8,6 @@ class NetChop(object):
     """
     Wrapper around netChop tool. Assumes netChop is in your PATH.
     """
-
     def predict_epitopes(self, sequences, threshold, min_len=8):
         """
         Return netChop predictions for each position in each sequence.
@@ -26,22 +25,22 @@ class NetChop(object):
         the cleavage probability for each position in the sequence.
         """
         with tempfile.NamedTemporaryFile(dir=config_setup['NETCHOP'], suffix=".fsa", mode="w") as input_fd:
-            print(f"Writing to {input_fd.name}...")
+        # temp_file = config_setup['NETCHOP'] / 'netchop_input.fsa'
+        # with open(temp_file, 'w') as input_fd:
             for (i, sequence) in enumerate(sequences):
-                print(f"\tseq{i}: {sequence}")
-                input_fd.write("> %d\n" % i)
-                input_fd.write(sequence)
-                input_fd.write("\n")
-            input_fd.flush()
+                _ = input_fd.write("> %d\n" % i)
+                _ = input_fd.write(sequence)
+                _ = input_fd.write("\n")
+            # input_fd.flush()
+            # print(str(temp_file))
 
             try:
-                output = subprocess.check_output(["netChop", input_fd.name])
+                output = subprocess.check_output(["netChop", str(input_fd.name)])
             except subprocess.CalledProcessError as e:
                 logging.error("Error calling netChop: %s:\n%s" % (e, e.output))
                 raise
 
         parsed = self.parse_netchop(output)
-
         assert len(parsed) == len(sequences), \
             "Expected %d results but got %d" % (
                 len(sequences), len(parsed))
@@ -51,7 +50,6 @@ class NetChop(object):
             proteosome = self.chop_protein(seq, [s > threshold for s in scores])
             filtered_proteosomes.append([e for e in proteosome if len(e) > min_len])
         return filtered_proteosomes
-
     @staticmethod
     def parse_netchop(netchop_output):
         """
@@ -70,7 +68,6 @@ class NetChop(object):
                     scores[-1].append(score)
                     line = next(line_iterator)
         return scores
-
     def chop_protein(self, seq, pos):
         # Generate subsequences using list comprehension and slicing
         start = 0

{geney-1.1.7.dist-info → geney-1.1.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.1.7
+Version: 1.1.9
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.1.7.dist-info → geney-1.1.9.dist-info}/RECORD

@@ -7,7 +7,7 @@ geney/config_setup.py,sha256=SePeooA4RWAtR_KAT1-W1hkD3MT5tH6YMyp80t_RNPQ,385
 geney/data_setup.py,sha256=DZeksRPr2ZT7bszMo33W0r3OwmqHokVXtZ4gx5Lu_Mo,10725
 geney/gtex.py,sha256=asL2lHyU5KsbWpV096vkf1Ka7hSo_RRfZqw7p5nERmE,1919
 geney/gtex_utils.py,sha256=asL2lHyU5KsbWpV096vkf1Ka7hSo_RRfZqw7p5nERmE,1919
-geney/netchop.py,sha256=h6hRkfYvmkU-ZI9Zeg5mW1fGUN4e97-Ar4r7aSGx7UE,2981
+geney/netchop.py,sha256=dYnhcc5p0ZBmVyEYl1Y0v7ImgM0MkTJ32eqbkH8Wabk,3050
 geney/oncosplice.py,sha256=Fyc_UtAhV3Pv0vk8V55rO_jnb2Dwj5sW98KVwP3PHwU,68964
 geney/oncosplice_pipeline.py,sha256=hpGqFHOdn8i8tvvs1-t3-G9Ko18zInwoDXBJbbrfbC4,68036
 geney/performance_utils.py,sha256=FQt7rA4r-Wuq3kceCxsSuMfj3wU1tMG8QnbL59aBohs,4700
@@ -43,7 +43,7 @@ geney/translation_initiation/resources/kozak_pssm.json,sha256=pcd0Olziutq-6H3mFW
 geney/translation_initiation/resources/tis_regressor_model.joblib,sha256=IXb4DUDhJ5rBDKcqMk9zE3ECTZZcdj7Jixz3KpoZ7OA,2592025
 geney/translation_termination/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 geney/translation_termination/tts_utils.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-geney-1.1.7.dist-info/METADATA,sha256=-arp47Qb2ah8D5x0TTBDaeUNu3kFwhmzwwBdiz5J0L8,1130
-geney-1.1.7.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
-geney-1.1.7.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.1.7.dist-info/RECORD,,
+geney-1.1.9.dist-info/METADATA,sha256=UhLRy4eXmizPtS10lnyzeZ7FG_4_zFOzf8Tw2t8xNV8,1130
+geney-1.1.9.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
+geney-1.1.9.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.1.9.dist-info/RECORD,,