Start test for future propagate_counts with relationships: #117

tests/test_propagate_counts_w_relationships.py

@@ -0,0 +1,45 @@
+#!/usr/bin/env python
+"""Test propagate_counts up relationships as well as parent-child links."""
+
+import sys
+import os
+# from itertools import combinations
+# import collections as cx
+
+from goatools.go_enrichment import GOEnrichmentStudy
+from goatools.base import get_godag
+from goatools.test_data.genes_NCBI_10090_ProteinCoding import GENEID2NT as GeneID2nt_mus
+from goatools.test_data.nature3102_goea import get_geneid2symbol
+from goatools.associations import get_assoc_ncbi_taxids
+
+def test_pc_w_rels(prt=sys.stdout):
+    """Test P-value calculations."""
+    results_r0 = _get_results(propagate_counts=True, relationships=False, prt=prt)
+    results_r1 = _get_results(propagate_counts=True, relationships=True, prt=prt)
+    _chk_results(results_r0, results_r1, prt)
+
+def _chk_results(results_r0, results_r1, prt):
+    """Test propagate_counts up relationships as well as parent-child links."""
+    prt.write('TBD: Compare results')
+    pass
+
+def _get_results(propagate_counts, relationships, prt=sys.stdout):
+    """Run a GOEA. Return results"""
+    taxid = 10090 # Mouse study
+    file_obo = os.path.join(os.getcwd(), "go-basic.obo")
+    obo_dag = get_godag(file_obo, prt, loading_bar=None)
+    geneids_pop = set(GeneID2nt_mus.keys())
+    assoc_geneid2gos = get_assoc_ncbi_taxids([taxid], loading_bar=None)
+    geneids_study = get_geneid2symbol("nbt.3102-S4_GeneIDs.xlsx")
+    goeaobj = GOEnrichmentStudy(
+        geneids_pop,
+        assoc_geneid2gos,
+        obo_dag,
+        propagate_counts=propagate_counts,
+        alpha=0.05,
+        methods=['fdr_bh'])
+    return goeaobj.run_study(geneids_study, prt=prt)
+
+
+if __name__ == '__main__':
+    test_pc_w_rels()