test for parameter log summary (pxlog)

FePhyFoFum · Feb 26, 2024 · 0ae664e · 0ae664e
1 parent 4af7272
commit 0ae664e
Showing 1 changed file with 6 additions and 0 deletions.
diff --git a/src/run_tests.py b/src/run_tests.py
@@ -211,6 +211,12 @@ def test_program(name):
         print("parameter log ", end = '')
         cm = "./pxlog -p TEST/run1.p TEST/run2.p -b 400 -n 10"
         t = 'Gen	LnL	LnPr	TL{all}	r(A<->C){all}	r(A<->G){all}	r(A<->T){all}	r(C<->G){all}	r(C<->T){all}	r(G<->T){all}	pi(A){all}	pi(C){all}	pi(G){all}	pi(T){all}	alpha{all}	pinvar{all}\n0	-2.562690e+04	-4.244089e+01	9.859853e+00	1.321215e-02	5.540706e-01	3.046823e-02	1.721216e-02	3.155399e-01	6.949704e-02	3.455151e-01	4.455032e-01	5.672251e-02	1.522591e-01	7.003904e-01	4.134683e-01\n1	-2.564363e+04	-3.385540e+01	8.861788e+00	1.597314e-02	5.405184e-01	3.572953e-02	1.538118e-02	3.098454e-01	8.255241e-02	3.383438e-01	4.445997e-01	6.011694e-02	1.569396e-01	7.525231e-01	4.174325e-01\n2	-2.564411e+04	-3.448828e+01	8.944435e+00	1.458647e-02	5.459096e-01	2.872731e-02	1.085169e-02	3.024874e-01	9.743752e-02	3.548307e-01	4.371532e-01	6.174098e-02	1.462752e-01	6.344983e-01	3.924460e-01\n3	-2.561863e+04	-3.780175e+01	9.315375e+00	1.358819e-02	5.484503e-01	2.921262e-02	1.526999e-02	3.124167e-01	8.106220e-02	3.516604e-01	4.366560e-01	6.137797e-02	1.503057e-01	6.601072e-01	3.928130e-01\n4	-2.562636e+04	-4.286557e+01	9.919687e+00	1.340228e-02	5.178548e-01	2.913669e-02	1.709175e-02	3.439590e-01	7.855543e-02	3.483430e-01	4.371204e-01	6.342031e-02	1.511163e-01	6.350827e-01	3.915076e-01\n5	-2.563020e+04	-2.769145e+01	8.224110e+00	1.577641e-02	5.576311e-01	3.089381e-02	9.919816e-03	3.176634e-01	6.811549e-02	3.528687e-01	4.393390e-01	6.275730e-02	1.450349e-01	6.266213e-01	4.008911e-01\n6	-2.561552e+04	-3.923375e+01	9.477967e+00	1.276876e-02	5.317353e-01	3.275137e-02	1.339039e-02	3.257596e-01	8.359464e-02	3.600337e-01	4.377344e-01	5.838327e-02	1.438486e-01	6.915539e-01	4.030057e-01\n7	-2.563452e+04	-3.925328e+01	9.485339e+00	1.164464e-02	5.139898e-01	3.236776e-02	1.466640e-02	3.338788e-01	9.345258e-02	3.563713e-01	4.399185e-01	5.766919e-02	1.460411e-01	6.481577e-01	4.187259e-01\n8	-2.562525e+04	-4.076892e+01	9.663887e+00	1.397800e-02	5.807593e-01	2.663268e-02	9.194246e-03	2.936051e-01	7.583059e-02	3.393248e-01	4.499280e-01	5.928337e-02	1.514639e-01	6.540484e-01	4.143338e-01\n9	-2.562177e+04	-3.821525e+01	9.362094e+00	1.134616e-02	5.635330e-01	3.136786e-02	1.478972e-02	2.936829e-01	8.528038e-02	3.391811e-01	4.535238e-01	6.084279e-02	1.464523e-01	6.687203e-01	4.171037e-01\n10	-2.563252e+04	-4.060590e+01	9.644269e+00	1.503387e-02	5.605209e-01	2.763069e-02	1.204396e-02	3.098828e-01	7.488771e-02	3.392548e-01	4.471247e-01	6.110044e-02	1.525201e-01	6.555609e-01	4.037897e-01\n11	-2.562664e+04	-4.213536e+01	9.833713e+00	1.232860e-02	5.395414e-01	3.024907e-02	1.121710e-02	3.268673e-01	7.979654e-02	3.408891e-01	4.480571e-01	5.879649e-02	1.522573e-01	6.098504e-01	4.188516e-01\n12	-2.563167e+04	-4.184690e+01	9.798107e+00	1.216011e-02	5.281554e-01	3.369355e-02	1.651959e-02	3.336440e-01	7.582734e-02	3.556323e-01	4.386915e-01	6.082072e-02	1.448555e-01	6.151424e-01	4.019154e-01\n13	-2.562311e+04	-3.511591e+01	9.011525e+00	1.420429e-02	5.225837e-01	3.129710e-02	1.897640e-02	3.393098e-01	7.362878e-02	3.610598e-01	4.292158e-01	6.198637e-02	1.477380e-01	6.576091e-01	4.184340e-01\n14	-2.562354e+04	-3.439340e+01	8.932346e+00	1.674036e-02	5.381113e-01	3.123254e-02	1.201223e-02	3.389401e-01	6.296347e-02	3.512489e-01	4.361070e-01	6.418764e-02	1.484565e-01	6.490354e-01	4.195533e-01\n15	-2.561774e+04	-4.104333e+01	9.693244e+00	1.356055e-02	5.555160e-01	3.013395e-02	1.497729e-02	3.087895e-01	7.702271e-02	3.417365e-01	4.459690e-01	6.307091e-02	1.492236e-01	6.828677e-01	4.044682e-01\n16	-2.561578e+04	-3.137908e+01	8.605127e+00	1.498821e-02	5.891174e-01	2.757067e-02	1.534648e-02	2.696136e-01	8.336370e-02	3.353194e-01	4.536863e-01	5.748396e-02	1.535103e-01	6.531047e-01	3.941014e-01\n17	-2.562464e+04	-3.780516e+01	9.306694e+00	1.253358e-02	5.801869e-01	2.503249e-02	1.866501e-02	2.952402e-01	6.834180e-02	3.418183e-01	4.492637e-01	5.784761e-02	1.510704e-01	7.389666e-01	4.123348e-01\n18	-2.562077e+04	-3.148056e+01	8.613531e+00	1.481873e-02	5.562068e-01	3.218332e-02	1.196085e-02	3.135224e-01	7.130797e-02	3.564275e-01	4.384962e-01	6.157918e-02	1.434971e-01	6.756563e-01	4.081317e-01\n19	-2.563194e+04	-3.882985e+01	9.430944e+00	1.473732e-02	5.618451e-01	3.124917e-02	1.722694e-02	3.139665e-01	6.097494e-02	3.486954e-01	4.429923e-01	5.866827e-02	1.496441e-01	6.902596e-01	4.020177e-01\n20	-2.562446e+04	-3.593565e+01	9.100935e+00	1.372513e-02	5.302188e-01	3.147862e-02	1.543002e-02	3.287349e-01	8.041257e-02	3.494219e-01	4.383438e-01	5.861659e-02	1.536177e-01	6.785744e-01	4.075729e-01\n21	-2.561437e+04	-3.343121e+01	8.819019e+00	1.364716e-02	5.058547e-01	3.713427e-02	1.752883e-02	3.592584e-01	6.657668e-02	3.573228e-01	4.355069e-01	6.246680e-02	1.447035e-01	7.196523e-01	4.225202e-01\n'
+        if not check_individual_results(cm, t):
+            res = False
+        print("summarize parameters ", end = '')
+        cm = "./pxlog -s -p TEST/run1.p TEST/run2.p -b 400 -n 10"
+        # expected results exclude leading spaces as these are apparently by p.communicate()
+        t = 'Mean       Median     Variance          ESS          ACT            N \nLnL               -25626.1     -25624.6      62.5741      20.2263       10.877           22\nLnPr              -37.3008     -37.8052      16.3973           22           10           22\nTL{all}            9.26836      9.36209     0.210032           22           10           22\nr(A<->C){all}    0.0138525    0.0137251  1.89553e-06           22           10           22\nr(A<->G){all}     0.546469      0.54845  0.000467429      15.1785      14.4942           22\nr(A<->T){all}    0.0307352    0.0312325   7.4479e-06           22           10           22\nr(C<->G){all}    0.0145305      0.01527   7.6606e-06           22           10           22\nr(C<->T){all}     0.317573      0.31554  0.000390585      14.8186      14.8462           22\nr(G<->T){all}    0.0768401    0.0770227  7.87827e-05      9.48203      23.2018           22\npi(A){all}        0.348423     0.349422  5.96536e-05      18.4677      11.9127           22\npi(C){all}        0.442042     0.439918  3.93657e-05       12.225      17.9959           22\npi(G){all}       0.0604063    0.0608428  4.45906e-06           22           10           22\npi(T){all}        0.149129     0.149644  1.30774e-05           22           10           22\nalpha{all}         0.66809     0.660107   0.00131491      11.9136      18.4663           22\npinvar{all}       0.407974     0.408132  9.37755e-05      14.7018      14.9641           22\n'
         if not check_individual_results(cm, t):
             res = False
         print_success(res)