Merge pull request #18 from luponzo86/master

update Oct. 2020
prody · Oct 8, 2020 · 483ef2c · 483ef2c
2 parents a3fa8b7 + 11e09c4
commit 483ef2c
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Showing 4 changed files with 22 additions and 8 deletions.
diff --git a/rhapsody/features/PolyPhen2.py b/rhapsody/features/PolyPhen2.py
@@ -225,10 +225,17 @@ def parsePolyPhen2output(pph2_output):
     # discard invalid lines
     lines = [l for l in lines if l.strip() and l[0] != '#']
     if not lines:
-        msg = ("PolyPhen-2's output is empty. Please make sure that: \n"
-               "1) variants' format is correct "
-               '(\"UniprotID pos wt_aa mut_aa\") \n'
-               "2) query contains *human* variants \n")
+        msg = (
+            "PolyPhen-2's output is empty. Please check file 'pph2-log.txt' "
+            "in the output folder for error messages from PolyPhen-2. \n"
+            "Typical errors include: \n"
+            "1) query contains *non-human* variants \n"
+            "2) variants' format is incorrect (e.g. "
+            '"UniprotID pos wt_aa mut_aa") \n'
+            "3) wild-type amino acids are in the wrong position on the "
+            "sequence (please refer to Uniprot's canonical isoform) \n"
+            "4) Uniprot accession number is not recognized by PolyPhen-2. \n"
+        )
         raise RuntimeError(msg)
     # define a structured array
     pl_dtype = np.dtype([(col, 'U25') for col in pph2_columns])

diff --git a/rhapsody/features/Uniprot.py b/rhapsody/features/Uniprot.py
@@ -33,10 +33,11 @@ def queryUniprot(*args, n_attempts=3, dt=1, **kwargs):
     attempt = 0
     while attempt < n_attempts:
         try:
-            print(f'attempt {attempt}')
             _ = openURL('http://www.uniprot.org/')
             break
         except:
+            LOGGER.info(
+                f'Attempt {attempt} to contact www.uniprot.org failed')
             attempt += 1
             time.sleep((attempt+1)*dt)
     else:
@@ -172,7 +173,13 @@ def alignCustomPDB(self, PDB, chain='all', title=None, recover=False):
         assert isinstance(title, str) or title is None
         # parse/import pdb and assign title
         if isinstance(PDB, str):
-            pdb = pd.parsePDB(PDB, subset='calpha')
+            try:
+                pdb = pd.parsePDB(PDB, subset='calpha')
+            except Exception as e:
+                msg = (
+                    'Unable to import PDB: PDB ID might be invalid or '
+                    f'PDB file might be corrupted. Error message: {e}')
+                LOGGER.error(msg)
             if title is None:
                 title = os.path.basename(PDB.strip())
                 title = title.replace(' ', '_')

diff --git a/rhapsody/predict/core.py b/rhapsody/predict/core.py
@@ -383,7 +383,7 @@ def getUniqueSAVcoords(self):
             except Exception:
                 LOGGER.warn(
                     'Invalid Uniprot coordinates at line {}: {}'.format(
-                    i, SAV['unique SAV coords']))
+                        i, SAV['unique SAV coords']))
                 uSAVcoords[i] = tuple(['?', '?', '?', -999, '?', '?'])
         return uSAVcoords
 

diff --git a/rhapsody/predict/main.py b/rhapsody/predict/main.py
@@ -53,7 +53,7 @@ def rhapsody(query, query_type='SAVs',
     :type custom_PDB: str, :class:`AtomGroup`
 
     :arg force_env: force a specific environment model for GNM/ANM
-      calculations, among ``'chain'``, ``'reduced'`` and ``'PolyPhen2'``.
+      calculations, among ``'chain'``, ``'reduced'`` and ``'sliced'``.
       If **None** (default), the model of individual dynamical features will
       match that found in the classifier's feature set
     :type force_env: str