Change fnc name to more accurately descriptive: print_summary->print_…

…date.
tanghaibao · Oct 13, 2018 · 329dadb · 329dadb
1 parent 5e1f05c
commit 329dadb
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Showing 5 changed files with 10 additions and 4 deletions.
diff --git a/goatools/cli/find_enrichment.py b/goatools/cli/find_enrichment.py
@@ -198,7 +198,7 @@ def _prt_results(self, goea_results):
         if min_ratio is not None:
             assert 1 <= min_ratio <= 2
         # print("MMMMMMMMMMMMMMMMMMMMMM", min_ratio)
-        self.objgoea.print_summary(min_ratio=min_ratio, pval=self.args.pval)
+        self.objgoea.print_date(min_ratio=min_ratio, pval=self.args.pval)
         results_adj = self.objgoea.get_adj_records(goea_results, min_ratio, self.args.pval)
         if results_adj:
             #### kws = {'indent':self.args.indent, 'itemid2name':self.itemid2name}

diff --git a/goatools/go_enrichment.py b/goatools/go_enrichment.py
@@ -503,8 +503,8 @@ def get_prtflds_default(results):
         return []
 
     @staticmethod
-    def print_summary(min_ratio=None, pval=0.05):
-        """Print summary."""
+    def print_date(min_ratio=None, pval=0.05):
+        """Print GOATOOLS version and the date the GOEA was run."""
         import goatools
 
         # Header contains provenance and parameters

diff --git a/goatools/ratio.py b/goatools/ratio.py
@@ -44,6 +44,10 @@ def is_ratio_different(min_ratio, study_go, study_n, pop_go, pop_n):
         return True
     stu_ratio = float(study_go) / study_n
     pop_ratio = float(pop_go) / pop_n
+    if stu_ratio == 0.0:
+        stu_ratio = 0.0000001
+    if pop_ratio == 0.0:
+        pop_ratio = 0.0000001
     if stu_ratio > pop_ratio:
         return stu_ratio / pop_ratio > min_ratio
     return pop_ratio / stu_ratio > min_ratio

diff --git a/tests/test_goea_local.py b/tests/test_goea_local.py
@@ -26,7 +26,8 @@ def test_goea_fdr_dflt():
     study_fin = "{REPO}/tests/data/small_study".format(REPO=REPO)
     study_ids = [line.rstrip() for line in open(study_fin)]
     goea_results = goeaobj.run_study(study_ids)
-    goeaobj.print_summary(goea_results)
+    goeaobj.print_results(goea_results)
+    goeaobj.print_date()
 
 def test_goea_local(log=sys.stdout):
     """Test GOEA with local multipletest correction methods for local."""

diff --git a/tests/test_print_results.py b/tests/test_print_results.py
@@ -29,6 +29,7 @@ def test_example():
     goea_results_sig = [r for r in goea_results_all if r.p_fdr_bh < 0.05]
     #goea_results_nt = MgrNtGOEAs(goea_results_sig).get_goea_nts_all()
     goeaobj.print_results(goea_results_sig)
+    goeaobj.print_date()
 
 
 if __name__ == '__main__':