Add quiet mode to run_goea

#133 (comment)

goatools/go_enrichment.py

@@ -292,14 +292,15 @@ def _remove_assc_goids(self, assoc, broad_goids):
     def run_study(self, study, **kws):
         """Run Gene Ontology Enrichment Study (GOEA) on study ids."""
         study_name = kws.get('name', 'current')
-        print('\nRun {OBJNAME} Gene Ontology Analysis: {STU} study set of {N} IDs ...'.format(
-            OBJNAME=self.name, N=len(study), STU=study_name))
+        log = self._get_log_or_prt(kws)
+        if log:
+            log.write('\nRun {OBJNAME} Gene Ontology Analysis: {STU} study set of {N} IDs ...'.format(
+                OBJNAME=self.name, N=len(study), STU=study_name))
         if not study:
             return []
         # Key-word arguments:
         methods = Methods(kws['methods']) if 'methods' in kws else self.methods
         alpha = kws['alpha'] if 'alpha' in kws else self.alpha
-        log = kws['log'] if 'log' in kws else self.log
         # Calculate uncorrected pvalues
         results = self.get_pval_uncorr(study, log)
         if not results:
@@ -326,6 +327,14 @@ def run_study(self, study, **kws):
         results.sort(key=lambda r: [r.enrichment, r.NS, r.p_uncorrected])
         return results # list of GOEnrichmentRecord objects
 
+    def _get_log_or_prt(self, kws):
+        """Allow either keyword, 'log', or 'prt' to be used to suppress or redirect printing"""
+        if 'log' in kws:
+            return kws['log']
+        if 'prt' in kws:
+            return kws['prt']
+        return self.log
+
     def run_study_nts(self, study, **kws):
         """Run GOEA on study ids. Return results as a list of namedtuples."""
         goea_results = self.run_study(study, **kws)

goatools/goea/go_enrichment_ns.py

@@ -15,9 +15,9 @@ class GOEnrichmentStudyNS:
     def __init__(self, pop, ns2assoc, godag, propagate_counts=True, alpha=.05, methods=None, **kws):
         self.ns2objgoea = self._ns2o(pop, ns2assoc, godag, propagate_counts, alpha, methods, **kws)
 
-    def run_study(self, study_ids):
+    def run_study(self, study_ids, **kws):
         """Run GOEAs for each namespace, BP MF CC"""
-        ns2results = {ns:o.run_study(study_ids) for ns, o in sorted(self.ns2objgoea.items())}
+        ns2results = {ns:o.run_study(study_ids, **kws) for ns, o in sorted(self.ns2objgoea.items())}
         return list(itertools.chain.from_iterable(ns2results.values()))
 
     def wr_xlsx(self, fout_xlsx, goea_results, **kws):

tests/test_goea_quiet.py

@@ -0,0 +1,63 @@
+"""Test that a Gene Ontology Enrichement Analysis can be run quietly"""
+
+import os
+from goatools.goea.go_enrichment_ns import GOEnrichmentStudyNS
+from goatools.anno.idtogos_reader import IdToGosReader
+from goatools.base import get_godag
+
+__copyright__ = "Copyright (C) 2010-present, H Tang et al., All rights reserved."
+
+REPO = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..")
+
+
+def test_goea_quiet():
+    """Test that a Gene Ontology Enrichement Analysis can be run quietly"""
+    goeaobj = _get_goeaobj()
+    study_fin = "{REPO}/tests/data/small_study".format(REPO=REPO)
+    study_ids = [line.rstrip() for line in open(study_fin)]
+    print('\nTEST 1: GOEA run_study(study_ids)')
+    goea_results1 = goeaobj.run_study(study_ids)
+    print('{N} GOEA results for verbose GOEA'.format(N=len(goea_results1)))
+
+    print('\nTEST 2: GOEA run_study(study_ids, prt=None)')
+    goea_results2 = goeaobj.run_study(study_ids, prt=None)
+    print('{N} GOEA results for quiet GOEA'.format(N=len(goea_results2)))
+
+    # Original keyword is 'log'
+    print('\nTEST 3: GOEA run_study(study_ids, log=None)')
+    goea_results3 = goeaobj.run_study(study_ids, log=None)
+    print('{N} GOEA results for quiet GOEA'.format(N=len(goea_results3)))
+
+
+    _chk_results(goea_results1, goea_results2)
+    _chk_results(goea_results1, goea_results3)
+
+
+def _get_goeaobj(methods=None):
+    """Test GOEA with method, fdr."""
+    # REad GODag
+    obo_fin = os.path.join(REPO, "go-basic.obo")
+    obo_dag = get_godag(obo_fin, loading_bar=None)
+    # Read association
+    fin_assc = "{REPO}/tests/data/small_association".format(REPO=REPO)
+    objanno = IdToGosReader(fin_assc, godag=obo_dag)
+    ns2assc = objanno.get_ns2assc()
+    popul_fin = "{REPO}/tests/data/small_population".format(REPO=REPO)
+    popul_ids = [line.rstrip() for line in open(popul_fin)]
+    goeaobj = GOEnrichmentStudyNS(popul_ids, ns2assc, obo_dag, methods=methods)
+    return goeaobj
+
+def _chk_results(results1, results2):
+    """Check that results match"""
+    # pylint: disable=line-too-long
+    for res1, res2 in zip(results1, results2):
+        assert res1.GO == res2.GO, '\nRES1: {R1}\nRES2: {R2}\n\n'.format(R1=res1, R2=res2)
+        assert res1.p_bonferroni == res2.p_bonferroni, '\nRES1: {R1}\nRES2: {R2}\n\n'.format(R1=res1, R2=res2)
+        assert res1.p_sidak == res2.p_sidak, '\nRES1: {R1}\nRES2: {R2}\n\n'.format(R1=res1, R2=res2)
+        assert res1.p_holm == res2.p_holm, '\nRES1: {R1}\nRES2: {R2}\n\n'.format(R1=res1, R2=res2)
+
+
+if __name__ == '__main__':
+    test_goea_quiet()
+
+# Copyright (C) 2010-present, H Tang et al., All rights reserved.