minor formatting

tanghaibao · Sep 27, 2023 · 8e86e44 · 8e86e44
1 parent ca4e1e3
commit 8e86e44
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Showing 3 changed files with 5 additions and 4 deletions.
diff --git a/goatools/anno/annoreader_base.py b/goatools/anno/annoreader_base.py
@@ -352,8 +352,8 @@ def chk_qualifiers(self):
             assert isinstance(
                 qual, set
             ), f"{self.name}: QUALIFIER MUST BE A LIST: {ntd}"
-            assert qual != set([""]), ntd
-            assert qual != set(["-"]), ntd
+            assert qual != {""}, ntd
+            assert qual != {"-"}, ntd
             assert "always" not in qual, "SPEC SAID IT WOULD BE THERE"
 
     def chk_godag(self):

diff --git a/goatools/cli/find_enrichment.py b/goatools/cli/find_enrichment.py
@@ -586,8 +586,8 @@ def _read_geneset(self, study_fn, pop_fn):
             pop |= study
             pop -= common
             study -= common
-            sys.stderr.write("removed %d overlapping items\n" % (len(common)))
-            sys.stderr.write("Set 1: {0}, Set 2: {1}\n".format(len(study), len(pop)))
+            sys.stderr.write(f"removed {len(common)} overlapping items\n")
+            sys.stderr.write(f"Set 1: {len(study)}, Set 2: {len(pop)}\n")
         return study, pop
 
     def _get_optional_attrs(self):

diff --git a/goatools/obo_parser.py b/goatools/obo_parser.py
@@ -415,6 +415,7 @@ def _init_depth(rec):
         for rec in self.values():
             if rec.level is None:
                 _init_level(rec)
+
             if rec.depth is None:
                 _init_depth(rec)