Added for testing GOEnrichmentStudy::print_results in issue #111

goatools/go_enrichment.py

@@ -91,7 +91,7 @@ def set_corrected_pval(self, nt_method, pvalue):
     def __str__(self, indent=False):
         field_data = [getattr(self, f, "n.a.") for f in self._fldsdefprt[:-1]] + \
                      [getattr(self, "p_{}".format(m.fieldname)) for m in self.method_flds] + \
-                     [", ".join(sorted(getattr(self, self._fldsdefprt[-1], set())))]
+                     [", ".join(str(e) for e in sorted(getattr(self, self._fldsdefprt[-1], set())))]
         fldsdeffmt = self._fldsdeffmt
         field_formatter = fldsdeffmt[:-1] + ["%.3g"]*len(self.method_flds) + [fldsdeffmt[-1]]
         self._chk_fields(field_data, field_formatter)

tests/test_print_results.py

@@ -0,0 +1,37 @@
+#!/usr/bin/env python
+"""Test GOEnrichmentStudy::print_results."""
+
+import os
+# from goatools.rpt.goea_nt_xfrm import MgrNtGOEAs  # get_goea_nts_all
+from goatools.test_data.genes_NCBI_10090_ProteinCoding import GENEID2NT as GeneID2nt_mus
+from goatools.test_data.nature3102_goea import get_geneid2symbol, get_goeaobj
+
+__copyright__ = "Copyright (C) 2016-2017, DV Klopfenstein, H Tang, All rights reserved."
+
+REPO = os.path.join(os.path.dirname(os.path.abspath(__file__)), "../")
+
+
+def test_example():
+    """Test GOEnrichmentStudy::print_results."""
+    # --------------------------------------------------------------------
+    # --------------------------------------------------------------------
+    # Gene Ontology Enrichment Analysis (GOEA)
+    # --------------------------------------------------------------------
+    # --------------------------------------------------------------------
+    taxid = 10090 # Mouse study
+    # Load ontologies, associations, and population ids
+    geneids_pop = GeneID2nt_mus.keys()
+    geneids2symbol_study = get_geneid2symbol("nbt.3102-S4_GeneIDs.xlsx")
+    geneids_study = geneids2symbol_study.keys()
+    goeaobj = get_goeaobj("fdr_bh", geneids_pop, taxid)
+    # Run GOEA on study
+    goea_results_all = goeaobj.run_study(geneids_study)
+    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)
+
+
+if __name__ == '__main__':
+    test_example()
+
+# Copyright (C) 2016-2017, DV Klopfenstein, H Tang, All rights reserved.