pylint. re-run travis.

goatools/go_enrichment.py

@@ -466,7 +466,7 @@ def prt_tsv(self, prt, goea_results, **kws):
         """Write tab-separated table data"""
         prt_flds = kws.get('prt_flds', self.get_prtflds_default(goea_results))
         tsv_data = MgrNtGOEAs(goea_results).get_goea_nts_prt(prt_flds, **kws)
-        RPT.prt_tsv(prt, tsv_data, prt_flds, **kws)
+        RPT.prt_tsv(prt, tsv_data, **kws)
 
     @staticmethod
     def get_ns2nts(results, fldnames=None, **kws):

tests/test_print_tsv.py

@@ -0,0 +1,39 @@
+#!/usr/bin/env python
+"""Test GOEnrichmentStudy::print_results."""
+
+import os
+import sys
+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 writing GOEA results into a tab-separated file."""
+    # --------------------------------------------------------------------
+    # --------------------------------------------------------------------
+    # Gene Ontology Enrichment Analysis (GOEA)
+    # --------------------------------------------------------------------
+    # --------------------------------------------------------------------
+    fout_tsv = os.path.join(REPO, 'goea_results.tsv')
+    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]
+    goeaobj.wr_tsv(fout_tsv, goea_results_sig)
+    assert os.path.exists(fout_tsv)
+    goeaobj.prt_tsv(sys.stdout, goea_results_sig)
+
+
+if __name__ == '__main__':
+    test_example()
+
+# Copyright (C) 2016-2017, DV Klopfenstein, H Tang, All rights reserved.