Uniprot (#21)

* added templates and config settings from ASAP Discovery to the docs to improve RTD; updated docstrings throughout; created uniprot module

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* corrected HumanKinaseInfo > KinaseInfo change in test

* added RTD badge to README

* fixed RTD link

* fixed RTD link - non-badge this time

* refactored code so that all existing work resides in databases sub-module

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* updated tests for cbioportal error

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

README.md

@@ -9,7 +9,7 @@ missense-kinase-toolkit
 
 An ETL pipeline package to facilitate structure-based ML for human kinase property prediction
 
-Additional documentation can be found [here](https://stackoverflow.com/questions/75922593/sphinx-readthedocs-and-package-version).
+Additional documentation can be found [here](https://missense-kinase-toolkit.readthedocs.io/en/latest/).
 
 ### Copyright
 

docs/_templates/custom-class-template.rst

@@ -4,6 +4,7 @@
 
 .. autoclass:: {{ objname }}
    :members:
+   :private-members:
    :show-inheritance:
    :inherited-members:
 

docs/_templates/custom-module-template.rst

@@ -1,5 +1,3 @@
-# courtesy of ASAP Discovery team
-
 {{ fullname | escape | underline}}
 
 .. automodule:: {{ fullname }}

docs/api.rst

@@ -6,4 +6,4 @@ API Documentation
    :template: custom-module-template.rst
    :recursive:
 
-   missense_kinase_toolkit
+   missense_kinase_toolkit.databases

docs/getting_started.rst

@@ -6,6 +6,8 @@ This page details how to get started with missense-kinase-toolkit.
 Installation
 ++++++++++++
 
+#TODO add pip install instructions
+
 We have used `poetry` as our default package manager for this project. Once you have cloned the repository and have either installed `poetry` locally or in your environment of interest, you can install the package by running the following command in the root directory of the repository using the provided `poetry.lock` file and the following command
 
 .. code-block:: bash

src/missense_kinase_toolkit/__init__.py

@@ -1,3 +0,0 @@
-from importlib.metadata import version
-
-__version__ = version("missense-kinase-toolkit")

src/missense_kinase_toolkit/databases/__init__.py

@@ -0,0 +1,3 @@
+from importlib.metadata import version
+
+__version__ = version("missense-kinase-toolkit")

src/missense_kinase_toolkit/cbioportal.py → src/missense_kinase_toolkit/databases/cbioportal.py

@@ -4,7 +4,7 @@
 from bravado.client import SwaggerClient
 from bravado.requests_client import RequestsClient
 
-from missense_kinase_toolkit import config, io_utils
+from missense_kinase_toolkit.databases import config, io_utils
 
 
 logger = logging.getLogger(__name__)
@@ -15,6 +15,8 @@ class cBioPortal():
     def __init__(self):
         """Initialize cBioPortal Class object.
 
+        Upon initialization, cBioPortal API is queried.
+
         Attributes
         ----------
         instance : str
@@ -27,7 +29,7 @@ def __init__(self):
         """
         self.instance = config.get_cbioportal_instance()
         self.url = f"https://{self.instance}/api/v2/api-docs"
-        self._cbioportal = self.get_cbioportal_api()
+        self._cbioportal = self.query_cbioportal_api()
 
     def _set_api_key(self):
         """Set API key for cBioPortal API.
@@ -51,8 +53,8 @@ def _set_api_key(self):
             print("No API token provided")
         return http_client
 
-    def get_cbioportal_api(self):
-        """Get cBioPortal API as bravado.client.SwaggerClient object.
+    def query_cbioportal_api(self):
+        """Queries cBioPortal API for instance as bravado.client.SwaggerClient object.
 
         Returns
         -------
@@ -95,6 +97,8 @@ def __init__(
     ) -> None:
         """Initialize Mutations Class object.
 
+        Upon initialization, cBioPortal API is queried and mutations for specificied study are retrieved.
+
         Parameters
         ----------
         study_id : str

src/missense_kinase_toolkit/cli/extract_cbioportal.py → src/missense_kinase_toolkit/databases/cli/extract_cbioportal.py

@@ -2,7 +2,7 @@
 
 import argparse
 
-from missense_kinase_toolkit import config, io_utils, cbioportal
+from missense_kinase_toolkit.databases import config, io_utils, cbioportal
 
 def parsearg_utils():
     parser = argparse.ArgumentParser(

src/missense_kinase_toolkit/cli/extract_kinase_annotations.py → src/missense_kinase_toolkit/databases/cli/extract_kinase_annotations.py

@@ -4,7 +4,7 @@
 
 import pandas as pd
 
-from missense_kinase_toolkit import config, io_utils, scrapers, klifs
+from missense_kinase_toolkit.databases import config, io_utils, scrapers, klifs
 
 def parsearg_utils():
     parser = argparse.ArgumentParser(

src/missense_kinase_toolkit/cli/transform_cbioportal.py → src/missense_kinase_toolkit/databases/cli/transform_cbioportal.py

@@ -2,7 +2,7 @@
 
 import argparse
 
-from missense_kinase_toolkit import config, io_utils
+from missense_kinase_toolkit.databases import config, io_utils
 
 
 def parsearg_utils():

src/missense_kinase_toolkit/config.py → src/missense_kinase_toolkit/databases/config.py

@@ -8,7 +8,7 @@
 """str: Environment variable for cBioPortal instance; if none provided, default is `www.cbioportal.org`"""
 CBIOPORTAL_TOKEN_VAR = "CBIOPORTAL_TOKEN"
 """str: Environment variable for cBioPortal token; if none provided, default is `None`"""
-REQUEST_CACHE_VAR = "REQUESTS_CACHE"
+REQUESTS_CACHE_VAR = "REQUESTS_CACHE"
 """str: Environment variable for request cache file prefix; if none provided, default is requests_cache"""
 
 
@@ -114,7 +114,7 @@ def maybe_get_cbioportal_token(
 
 
 def set_request_cache(
-    val: bool
+    val: str
 ) -> None:
     """Set the request cache path in environment variables.
 
@@ -128,8 +128,7 @@ def set_request_cache(
     None
 
     """
-    #TODO: val should be bool but doesn't work with env, fix
-    os.environ[REQUEST_CACHE_VAR] = str(val)
+    os.environ[REQUESTS_CACHE_VAR] = val
 
 
 def maybe_get_request_cache(
@@ -143,6 +142,6 @@ def maybe_get_request_cache(
 
     """
     try:
-        return os.environ[REQUEST_CACHE_VAR]
+        return os.environ[REQUESTS_CACHE_VAR]
     except KeyError:
         return None

src/missense_kinase_toolkit/hgnc.py → src/missense_kinase_toolkit/databases/hgnc.py

@@ -1,6 +1,6 @@
 import requests
 
-from missense_kinase_toolkit import requests_wrapper, utils_requests
+from missense_kinase_toolkit.databases import requests_wrapper, utils_requests
 
 
 def maybe_get_symbol_from_hgnc_search(

src/missense_kinase_toolkit/klifs.py → src/missense_kinase_toolkit/databases/klifs.py

@@ -11,6 +11,8 @@ class KLIFS():
     def __init__(self):
         """Initialize KLIFS Class object.
 
+        Upon initialization, KLIFS API is queried.
+
         Attributes
         ----------
         url : str
@@ -20,9 +22,9 @@ def __init__(self):
 
         """
         self.url = "https://dev.klifs.net/swagger_v2/swagger.json"
-        self._klifs = self.get_klifs_api()
+        self._klifs = self.query_klifs_api()
 
-    def get_klifs_api(self):
+    def query_klifs_api(self):
         """Get KLIFS API as bravado.client.SwaggerClient object.
 
         Returns
@@ -60,6 +62,8 @@ def __init__(
     ) -> None:
         """Initialize KinaseInfo Class object.
 
+        Upon initialization, KLIFS API is queried and kinase information for specificied kinase is retrieved.
+
         Parameters
         ----------
         kinase_name : str
@@ -80,9 +84,9 @@ def __init__(
         super().__init__()
         self.kinase_name = kinase_name
         self.species = species
-        self._kinase_info = self.get_kinase_info()
+        self._kinase_info = self.query_kinase_info()
 
-    def get_kinase_info(
+    def query_kinase_info(
         self
     ) -> dict[str, str | int | None]:
         """Get information about a kinase from KLIFS.
@@ -133,3 +137,7 @@ def get_kinase_name(self):
     def get_species(self):
         """Get species of the kinase."""
         return self.species
+
+    def get_kinase_info(self):
+        """Get information about the kinase."""
+        return self._kinase_info

src/missense_kinase_toolkit/pfam.py → src/missense_kinase_toolkit/databases/pfam.py

@@ -2,7 +2,7 @@
 
 import pandas as pd
 
-from missense_kinase_toolkit import requests_wrapper, utils_requests
+from missense_kinase_toolkit.databases import requests_wrapper, utils_requests
 
 
 def retrieve_pfam(

src/missense_kinase_toolkit/scrapers.py → src/missense_kinase_toolkit/databases/scrapers.py

@@ -1,6 +1,6 @@
 import pandas as pd
 
-from missense_kinase_toolkit import requests_wrapper
+from missense_kinase_toolkit.databases import requests_wrapper
 
 
 def kinhub(
@@ -52,6 +52,7 @@ def kinhub(
     df_kinhub = pd.DataFrame.from_dict(dict_kinhub)
     # df_kinhub = clean_names(df_kinhub)
 
+    # aggregate rows with the same HGNC Name (e.g., multiple kinase domains like JAK)
     list_cols = df_kinhub.columns.to_list()
     list_cols.remove("HGNC Name")
     df_kinhub_agg = df_kinhub.groupby(["HGNC Name"], as_index=False, sort=False).agg(set)

tests/test_databases.py

@@ -0,0 +1,109 @@
+"""
+Unit and regression test for the missense_kinase_toolkit package.
+"""
+
+# Import package, test suite, and other packages as needed
+import pytest
+
+
+def test_missense_kinase_toolkit_database_imported():
+    """Test if module is imported."""
+    import sys
+    import missense_kinase_toolkit.databases
+
+    assert "missense_kinase_toolkit.databases" in sys.modules
+
+
+def test_config():
+    from missense_kinase_toolkit.databases import config
+
+    # test that the function to set the output directory works
+    config.set_output_dir("test")
+    assert config.get_output_dir() == "test"
+
+    # test that the function to set the request cache works
+    config.set_request_cache("test")
+    assert config.maybe_get_request_cache() == "test"
+
+    # test that the function to set the cBioPortal instance works
+    config.set_cbioportal_instance("test")
+    assert config.get_cbioportal_instance() == "test"
+
+    # test that the function to set the cBioPortal token works
+    config.set_cbioportal_token("test")
+    assert config.maybe_get_cbioportal_token() == "test"
+
+
+def test_cbioportal():
+    from missense_kinase_toolkit.databases import config, cbioportal
+
+    config.set_cbioportal_instance("www.cbioportal.org")
+
+    # test that the function to set the API key for cBioPortal works
+    # cbioportal.cBioPortal()._set_api_key()
+
+    # test that the function to query the cBioPortal API works
+    cbioportal_instance = cbioportal.cBioPortal()
+
+    # test that server status is up
+    assert cbioportal_instance._cbioportal.Server_running_status.getServerStatusUsingGET().response().result["status"] == "UP"
+
+    # test that Zehir cohort is available
+    list_studies = cbioportal_instance._cbioportal.Studies.getAllStudiesUsingGET().result()
+    list_study_ids = [study.studyId for study in list_studies]
+    assert "msk_impact_2017" in list_study_ids
+
+
+def test_io_utils():
+    from missense_kinase_toolkit.databases import io_utils
+    import pandas as pd
+    import os
+
+    os.environ["OUTPUT_DIR"] = "."
+
+    # test that the functions to save and load dataframes work
+    df = pd.DataFrame({"A": [1, 2, 3], "B": [4, 5, 6]})
+    io_utils.save_dataframe_to_csv(df, "test1.csv")
+    df_read = io_utils.load_csv_to_dataframe("test1.csv")
+    assert df.equals(df_read)
+
+    # test that the function to concatenate csv files with glob works
+    io_utils.save_dataframe_to_csv(df, "test2.csv")
+    df_concat = io_utils.concatenate_csv_files_with_glob("*test*.csv")
+    assert df_concat.equals(pd.concat([df, df]))
+
+    # remove the files created
+    os.remove("test1.csv")
+    os.remove("test2.csv")
+
+    # test that the function to convert a string to a list works
+    assert io_utils.convert_str2list("a,b,c") == ["a", "b", "c"]
+    assert io_utils.convert_str2list("a, b, c") == ["a", "b", "c"]
+
+
+def test_kinhub_scraper():
+    from missense_kinase_toolkit.databases import scrapers
+
+    df_kinhub = scrapers.kinhub()
+
+    assert df_kinhub.shape[0] == 517
+    assert df_kinhub.shape[1] == 8
+    assert "HGNC Name" in df_kinhub.columns
+    assert "UniprotID" in df_kinhub.columns
+
+
+def test_klifs_KinaseInfo():
+    from missense_kinase_toolkit.databases import klifs
+
+    dict_egfr = klifs.KinaseInfo("EGFR")._kinase_info
+
+    assert dict_egfr["family"]      ==      "EGFR"
+    assert dict_egfr["full_name"]   ==      "epidermal growth factor receptor"
+    assert dict_egfr["gene_name"]   ==      "EGFR"
+    assert dict_egfr["group"]       ==      "TK"
+    assert dict_egfr["iuphar"]      ==      1797
+    assert dict_egfr["kinase_ID"]   ==      406
+    assert dict_egfr["name"]        ==      "EGFR"
+    assert dict_egfr["pocket"]      ==      "KVLGSGAFGTVYKVAIKELEILDEAYVMASVDPHVCRLLGIQLITQLMPFGCLLDYVREYLEDRRLVHRDLAARNVLVITDFGLA"
+    assert dict_egfr["species"]     ==      "Human"
+    assert dict_egfr["uniprot"]     ==      "P00533"