Added test

makefile

@@ -197,6 +197,7 @@ clobber:
 #    tests/test_gosubdag_children.py \
 
 NOSETESTS := \
+    tests/test_dcnt_r01.py \
     tests/test_grprobj.py \
     tests/test_grpr_get_sections_2d.py \
     tests/test_sorter.py \

tests/test_dcnt_r01.py

@@ -0,0 +1,109 @@
+#!/usr/bin/env python
+"""Ancestors/Descendants."""
+
+import os
+import sys
+import timeit
+import numpy as np
+from numpy.random import shuffle
+from scipy import stats
+
+from goatools.base import download_go_basic_obo
+from goatools.obo_parser import GODag
+from goatools.test_data.godag_timed import prt_hms
+from goatools.gosubdag.gosubdag import GoSubDag
+
+
+def test_go_pools():
+    """Print a comparison of GO terms from different species in two different comparisons."""
+    objr = _Run()
+    # Check that subset GoSubDags have the same ancestors/descendants as Full GoSubDag
+    for qty in np.random.randint(10, 100, size=10):
+        print("")
+        goids = objr.get_goids_rand(qty)
+        # No relationships loaded; GoSubDag subset equivalent to Full subset?
+        gosubdag_r0 = objr.get_gosubdag_r0(goids)
+        for goid in gosubdag_r0.go2obj:
+            r0_u = gosubdag_r0.rcntobj.go2parents[goid]
+            r0_d = gosubdag_r0.rcntobj.go2descendants[goid]
+            assert r0_u == objr.gosubdag_r0.rcntobj.go2parents[goid]
+            assert r0_d == objr.gosubdag_r0.rcntobj.go2descendants[goid]
+        # All relationships loaded; GoSubDag(r0) vs. GoSubDag(r1)
+        gosubdag_r1 = objr.get_gosubdag_r1(goids)
+        assert gosubdag_r0.go_sources == gosubdag_r1.go_sources
+        assert set(gosubdag_r0.go2obj).issubset(gosubdag_r1.go2obj)
+        cnts = {'r0_u':[], 'r1_u':[], 'r0_d':[], 'r1_d':[]}
+        for goid in gosubdag_r0.go2obj:
+            r0_u = gosubdag_r0.rcntobj.go2parents[goid]
+            r0_d = gosubdag_r0.rcntobj.go2descendants[goid]
+            r1_u = gosubdag_r1.rcntobj.go2parents[goid]
+            r1_d = gosubdag_r1.rcntobj.go2descendants[goid]
+            assert r0_d.issubset(r1_d), "R1({}) R0({})".format(len(r1_d), len(r0_d))
+            assert r0_u.issubset(r1_u), "R1({}) R0({})".format(len(r1_u), len(r0_u))
+            cnts['r0_u'].append(len(r0_u))
+            cnts['r1_u'].append(len(r1_u))
+            cnts['r0_d'].append(len(r0_d))
+            cnts['r1_d'].append(len(r1_d))
+        objr.prt_cnts(cnts)
+
+
+class _Run(object):
+    """Group entire go-basic.obo"""
+
+    obo = os.path.join(os.path.dirname(os.path.abspath(__file__)), "../../go-basic.obo")
+
+    def __init__(self):
+        download_go_basic_obo(self.obo, sys.stdout, loading_bar=None)
+        self.godag_r0 = GODag("go-basic.obo")
+        self.godag_r1 = GODag("go-basic.obo", optional_attrs=set(['relationship']))
+        self.goids = list(set(o.id for o in self.godag_r0.values()))
+        # GoSubDag (plain)
+        tic = timeit.default_timer()
+        self.gosubdag_r0 = GoSubDag(self.goids, self.godag_r0, prt=None)
+        prt_hms(tic, "GoSubDag r0 {N:4} GOs {S:3} srcs".format(
+            N=len(self.gosubdag_r0.go2obj), S=len(self.gosubdag_r0.go_sources)))
+        # GoSubDag with relationships
+        self.gosubdag_r1 = GoSubDag(self.goids, self.godag_r1, prt=None, relationships=True)
+        prt_hms(tic, "GoSubDag r1 {N:4} GOs {S:3} srcs".format(
+            N=len(self.gosubdag_r1.go2obj), S=len(self.gosubdag_r1.go_sources)))
+
+    def prt_cnts(self, cnts):
+        """Compare ancestor/descendant counts with relatives=False/True."""
+        k2v = {k:self.str_stats(v) for k, v in cnts.items()}
+        print(k2v)
+
+    @staticmethod
+    def str_stats(vals):
+        """Print statistics on values."""
+        ntd = stats.describe(vals)
+        std = int(round(np.sqrt(ntd.variance)))
+        return "({m} {M}) STD={STD:,}".format(m=ntd.minmax[0], M=ntd.minmax[1], STD=std)
+
+    def get_gosubdag_r0(self, goids):
+        """Return a GoSubDag with N randomly chosen GO sources."""
+        tic = timeit.default_timer()
+        gosubdag = GoSubDag(goids, self.godag_r0, relationships=None,
+                            #rcntobj=self.gosubdag_r0.rcntobj,
+                            prt=None)
+        prt_hms(tic, "GoSubDag r0 {N:4} GOs {S:3} srcs".format(
+            N=len(gosubdag.go2obj), S=len(gosubdag.go_sources)))
+        return gosubdag
+
+    def get_gosubdag_r1(self, goids):
+        """Return a GoSubDag with N randomly chosen GO sources."""
+        tic = timeit.default_timer()
+        gosubdag = GoSubDag(goids, self.godag_r1, relationships=True,
+                            #rcntobj=self.gosubdag_r1.rcntobj,
+                            prt=None)
+        prt_hms(tic, "GoSubDag r1 {N:4} GOs {S:3} srcs".format(
+            N=len(gosubdag.go2obj), S=len(gosubdag.go_sources)))
+        return gosubdag
+
+    def get_goids_rand(self, qty):
+        """Return N randomly chosen GO IDs."""
+        shuffle(self.goids)
+        return self.goids[:qty]
+
+
+if __name__ == '__main__':
+    test_go_pools()