Merge pull request #2 from MPI-Dortmund/thorstenwagner-patch-1

Add unit tests and automatic versioning + deployment

.github/workflows/pylint.yml

@@ -0,0 +1,53 @@
+name: Pylint
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10"]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pylint pytest pytest-coverage
+        pip install .
+    - name: Analysing the code with pylint
+      run: |
+        pylint -E $(git ls-files '*.py')
+    - name: Tests
+      run: |
+        pytest -v --cov=./ --cov-report=xml --cov-config=.coveragerc
+  deploy:
+      # this will run when you have tagged a commit, starting with "v*"
+      # and requires that you have put your twine API key in your
+      # github secrets (see readme for details)
+      needs: [ build ]
+      runs-on: ubuntu-latest
+      if: contains(github.ref, 'tags')
+      steps:
+        - uses: actions/checkout@v3
+        - name: Set up Python
+          uses: actions/setup-python@v4
+          with:
+            python-version: "3.x"
+        - name: Install dependencies
+          run: |
+            python -m pip install --upgrade pip
+            pip install -U setuptools setuptools_scm wheel twine build
+  
+        - name: Build and publish
+          env:
+            TWINE_USERNAME: __token__
+            TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
+          run: |
+            git tag
+            python -m build .
+            twine upload dist/*

README.md

@@ -43,7 +43,7 @@ options:
   --maxacid MAXACID  Maximum squence number to use. (default: None)
 ```
 
-You can provide the optional argument `--pdbpath` if you want to use an experimental PDB, otherwise it will instead download the alphafold predicted PDB. One example could be:
+You can provide the optional argument `--pdbpath` if you want to use an experimental PDB, otherwise it will instead download the alphafold predicted PDB.
 
 For example, to reproduce [Figure 3D](https://www.science.org/doi/10.1126/science.adg7492#F3) (the middle one) and the generate the PDB shown in [Figure 3E](https://www.science.org/doi/10.1126/science.adg7492#F3) do:
 

missense/missense.py

@@ -405,9 +405,9 @@ def get_data_tuple(uniprot_id: str):
     """
     Extracts the raw data for the plot from the tsv file.
     """
-    with open(os.path.join(tempfile.gettempdir(), "alpha.tsv")) as f:
+    with open(os.path.join(tempfile.gettempdir(), "alpha.tsv"), encoding="utf-8") as f:
         doc = f.read()
-        m = re.findall(uniprot_id.upper() + "\t(.\d+.)\t(\d.\d+)", doc)
+        m = re.findall(uniprot_id.upper() + r"\t(.\d+.)\t(\d.\d+)", doc)
     pos_to_val = []
 
     for g in m:
@@ -424,7 +424,7 @@ def download_missense_data():
     '''
     alphafile=os.path.join(tempfile.gettempdir(), "alpha.tsv")
     if not os.path.exists(alphafile):
-        url = ("https://zenodo.org/record/8208688/files/AlphaMissense_aa_substitutions.tsv.gz?download=1/")
+        url = "https://zenodo.org/record/8208688/files/AlphaMissense_aa_substitutions.tsv.gz?download=1/"
         filename = os.path.join(tempfile.gettempdir(), "alpha.tsv.gz")
         print("Download to", filename, " ...")
         urlretrieve(url, filename)
@@ -439,6 +439,9 @@ def download_missense_data():
 
 
 def create_parser() -> argparse.ArgumentParser:
+    '''
+    Create the argument parser
+    '''
     parser = argparse.ArgumentParser(
             description="AlphaMissense plot and pdb generator",
             formatter_class=argparse.ArgumentDefaultsHelpFormatter,
@@ -472,8 +475,12 @@ def create_parser() -> argparse.ArgumentParser:
 
 
 def make_and_save_plot(pos_to_val, out_file: str, maxpos: int =None) -> np.array:
+    """
+    Create the plot at saves it to disk.
+    :return The raw data for the plot
+    """
     img = gen_image(pos_to_val)
-    fig, ax = pyplot.subplots(1, 1)
+    _, ax = pyplot.subplots(1, 1)
 
     ax.imshow(img, aspect='auto', interpolation='none', cmap="bwr")
 
@@ -498,26 +505,32 @@ def make_and_save_plot(pos_to_val, out_file: str, maxpos: int =None) -> np.array
     return img
 
 def get_chain(uniprot_id,pdb_pth:str):
+    '''
+    A PDB might have multiple chains, where only one belongs to a certain UNIPROT-ID. This function tries to retrieve the corresponding chain.
+    '''
     with open(pdb_pth, mode="rt", encoding="utf-8") as f:
         doc = f.read()
-        p = r"DBREF\s+." + "{4}" + f"\s(.).+{uniprot_id.upper()}"
+        p = r"DBREF\s+." + "{4}" + rf"\s(.).+{uniprot_id.upper()}"
         return re.findall(p,doc)[0]
 
 def create_modified_pdb(img: np.array, uniprot_id: str, output_path: str, pdb_pth=None, chain=None):
+    '''
+    Replaces the bfactor column with the patho score.
+    '''
     if pdb_pth is not None and os.path.isfile(pdb_pth):
         target_pdb = pdb_pth
 
     else:
         target_pdb = os.path.join(tempfile.gettempdir(), "AF.pdb")
         api_url = f"https://alphafold.ebi.ac.uk/api/prediction/{uniprot_id.upper()}"
-        response = requests.get(api_url)
+        response = requests.get(api_url, timeout=20)
         r = response.json()
         urllib.request.urlretrieve(r[0]['pdbUrl'], target_pdb)
 
     mean_per_pos = img.mean(axis=0)
 
-    with open(target_pdb) as f:
-        with open(output_path, 'w+') as out_file:
+    with open(target_pdb, encoding="utf-8") as f:
+        with open(output_path, 'w+', encoding="utf-8") as out_file:
             for line in f:
                 if line.startswith("ATOM "):
                     if chain is not None and line[21] != chain:
@@ -534,33 +547,33 @@ def create_modified_pdb(img: np.array, uniprot_id: str, output_path: str, pdb_pt
                 else:
                     out_file.write(f'{line}')
 
-
-def _main_():
-    args = create_parser().parse_args()
+def _run(uniprot_id: str, output_path: str, pdbpath: str, maxacid: int):
     download_missense_data()
-    os.makedirs(args.output_path, exist_ok=True)
+    os.makedirs(output_path, exist_ok=True)
 
-    # Wenn pdb existiert
     chain = None
-    if args.pdbpath is not None and os.path.exists(args.pdbpath):
+    if pdbpath is not None and os.path.exists(pdbpath):
         try:
-            chain = get_chain(args.uniprot_id, args.pdbpath)
-        except:
-            print(f"Cant find chain for {args.uniprot_id} in {args.pdbpath}")
+            chain = get_chain(uniprot_id, pdbpath)
+        except IndexError:
+            print(f"Cant find chain for {uniprot_id} in {pdbpath}")
             sys.exit(1)
 
-    pos_to_val = get_data_tuple(args.uniprot_id)
-
-
+    pos_to_val = get_data_tuple(uniprot_id)
 
-    out_fig_pth = os.path.join(args.output_path, f"{args.uniprot_id}.pdf")
-    img_raw_data = make_and_save_plot(pos_to_val, out_fig_pth, args.maxacid)
+    out_fig_pth = os.path.join(output_path, f"{uniprot_id}.pdf")
+    img_raw_data = make_and_save_plot(pos_to_val, out_fig_pth, maxacid)
     print(f"Save plot to {out_fig_pth}")
-    out_pdb_pth = os.path.join(args.output_path, f'{args.uniprot_id}-edit.pdb')
-    create_modified_pdb(img_raw_data, args.uniprot_id, out_pdb_pth, args.pdbpath, chain)
+    out_pdb_pth = os.path.join(output_path, f'{uniprot_id}-edit.pdb')
+    create_modified_pdb(img_raw_data, uniprot_id, out_pdb_pth, pdbpath, chain)
     print(f"Save modified PDB to {out_pdb_pth}")
 
+def _main_():
+    args = create_parser().parse_args()
+    _run(args.uniprot_id, args.output_path, args.pdbpath, args.maxacid)
+
+
 
 
 if __name__ == "__main__":
-    _main_()
+    _main_()