Merge branch 'main' into feature-modelcif

tests/test_provean_anno.py

@@ -19,7 +19,7 @@ class TestProveanAnno(unittest.TestCase):
         self.nrdb_prefix = "nr"
         self.nrdb = os.path.join(self.nrdb_dir, self.nrdb_prefix)
         os.makedirs(self.nrdb_dir)
-        open(self.nrdb, "a").close()
+        open(self.nrdb, 'a').close()
 
         # generate fake executables
         self.provean_exe = os.path.join(self.tmp_dir.name, "provean")
@@ -66,6 +66,16 @@ class TestProveanAnno(unittest.TestCase):
                 cdhit_exe=self.cdhit_exe,
                 blastdbcmd_exe=self.blastdbcmd_exe,
             )
+        # try only with nrdb dir but without prefix
+        with self.assertRaises(ValueError):
+            ProveanVarSeqAnno(
+                self.nrdb_dir,
+                tmp_dir=self.tmp_dir.name,
+                provean_exe=self.provean_exe,
+                psiblast_exe=self.psiblast_exe,
+                cdhit_exe=self.cdhit_exe,
+                blastdbcmd_exe=self.blastdbcmd_exe,
+            )
         ProveanVarSeqAnno(
             self.nrdb,
             tmp_dir=self.tmp_dir.name,

var3d/var_seq_anno.py

@@ -96,7 +96,11 @@ class ProveanVarSeqAnno(VarSeqAnno):
                 f"not exist ({self.blast_nrdb_dirname})"
             )
         blast_files = os.listdir(self.blast_nrdb_dirname)
-        n = sum([f.startswith(self.blast_nrdb_prefix) for f in blast_files])
+        n = 0
+        for f in blast_files:
+            if f.startswith(self.blast_nrdb_prefix) and \
+               os.path.isfile(os.path.join(self.blast_nrdb_dirname,f)):
+               n += 1
         if n == 0:
             raise ValueError(
                 f"No files starting with expected prefix "