Addressing issues #4, #5, #6 and #7

klamt-lab · Oct 13, 2020 · fb58137 · fb58137
1 parent 786ad0c
commit fb58137
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Showing 4 changed files with 24 additions and 9 deletions.
diff --git a/autopacmen/data_parse_brenda_textfile.py b/autopacmen/data_parse_brenda_textfile.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 #
-# Copyright 2019 PSB
+# Copyright 2019-2020 PSB
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -42,7 +42,7 @@
                    "must not have been changed.")
 @click.option("--json_output_path",
               required=True,
-              type=click.Path(exists=True, dir_okay=True),
+              type=click.Path(file_okay=True, dir_okay=True, writable=True),
               prompt="JSON output path",
               help="The full path for the more machine-readable JSON file of the"
                    " BRENDA database text file shall be placed. The resulting JSON "

diff --git a/autopacmen/modeling_get_reactions_kcat_mapping.py b/autopacmen/modeling_get_reactions_kcat_mapping.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 #
-# Copyright 2019 PSB
+# Copyright 2019-2020 PSB
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -56,9 +56,11 @@
 @click.option("--protein_kcat_database_path",
               required=True,
               type=click.Path(exists=True, file_okay=True, dir_okay=True),
+              default="",
               prompt="protein kcat database path",
               help="Full path to the custom user-defined kcat<->protein JSON. It must be a dictionary containing the protein names"
-                   "(as given in the metabolic network's gene rules) as keys and associated kcats as children. See this script's description for more.")
+                   "(as given in the metabolic network's gene rules) as keys and associated kcats as children. See this script's description for more."
+                   "Default is '', which means that no user-defined database is given.")
 @click.option("--type_of_kcat_selection",
               required=True,
               type=str,

diff --git a/autopacmen/submodules/create_combined_kcat_database.py b/autopacmen/submodules/create_combined_kcat_database.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 #
-# Copyright 2019 PSB
+# Copyright 2019-2020 PSB
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -65,9 +65,21 @@ def create_combined_kcat_database(sabio_rk_kcat_database_path: str, brenda_kcat_
     combined_database: Dict[str, Dict[str, Any]] = {}
     # Go through each EC number :D...
     for ec_number_key in ec_number_keys:
-        # Get the wildcard status (i.e., found with a * wildcard?)
-        is_sabio_rk_from_wildcard: bool = sabio_rk_database[ec_number_key]["WILDCARD"]
-        is_brenda_from_wildcard: bool = brenda_database[ec_number_key]["WILDCARD"]
+        # Get the wildcard status (i.e., found with a * wildcard?) and check if the EC number occurs anywhere...
+        # ...for SABIO-RK
+        if ec_number_key not in sabio_rk_database.keys():
+            print(f"WARNING: EC number {ec_number_key} could not be found in SABIO-RK, even with wildcards")
+            print("Possible reasons: The EC number format is invalid or there was an SABIO-RK API error")
+            is_sabio_rk_from_wildcard = True  # Let the combined database ignore this entry
+        else:
+            is_sabio_rk_from_wildcard = sabio_rk_database[ec_number_key]["WILDCARD"]
+        # ...and for BRENDA
+        if ec_number_key not in brenda_database.keys():
+            print(f"WARNING: EC number {ec_number_key} could not be found in SABIO-RK, even with wildcards")
+            print("Possible reason: The EC number format is invalid")
+            is_brenda_from_wildcard = True  # Let the combined database ignore this entry
+        else:
+            is_brenda_from_wildcard = brenda_database[ec_number_key]["WILDCARD"]
 
         # If both are from wildcards, ignore them :3
         if (is_sabio_rk_from_wildcard) and (is_brenda_from_wildcard):

diff --git a/setup.py b/setup.py
@@ -5,13 +5,14 @@
 
 setuptools.setup(
     name="autopacmen-Paulocracy",
-    version="0.5.5",
+    version="0.5.6",
     author="Paulocracy",
     author_email="[email protected]",
     description="The AutoPACMEN package",
     long_description=long_description,
     long_description_content_type="text/markdown",
     url="https://github.com/Paulocracy/autopacmen",
+    packages=setuptools.find_packages(),
     classifiers=[
         "Programming Language :: Python :: 3",
         "License :: OSI Approved :: Apache Software License",