diff options
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/unit/computations/test_partial_correlations.py | 82 |
1 files changed, 79 insertions, 3 deletions
diff --git a/tests/unit/computations/test_partial_correlations.py b/tests/unit/computations/test_partial_correlations.py index 981801a..28c9548 100644 --- a/tests/unit/computations/test_partial_correlations.py +++ b/tests/unit/computations/test_partial_correlations.py @@ -6,6 +6,8 @@ from unittest import TestCase import pandas from gn3.settings import ROUND_TO +from gn3.function_helpers import compose +from gn3.data_helpers import partition_by from gn3.computations.partial_correlations import ( fix_samples, control_samples, @@ -120,6 +122,80 @@ def parse_test_data_csv(filename): "result": round(float(line["result"]), ROUND_TO) } for line in lines) +def parse_method(key_value): + """Parse the partial correlation method""" + key, value = key_value + if key == "method": + methods_dict = {"p": "pearson", "k": "kendall", "s": "spearman"} + return (key, methods_dict[value]) + return key_value + +def parse_count(key_value): + """Parse the value of count into an integer""" + key, value = key_value + if key == "count": + return (key, int(value)) + return key_value + +def parse_xyz(key_value): + """Parse the values of x, y, and z* items into sequences of floats""" + key, value = key_value + if (key in ("x", "y", "z")) or key.startswith("input.z"): + return ( + key.replace("input", "").replace(".", ""), + tuple(float(val.strip("\n\t ")) for val in value.split(","))) + return key_value + +def parse_rm(key_value): + """Parse the rm value into a python True/False value.""" + key, value = key_value + if key == "rm": + return (key, value == "TRUE") + return key_value + +def parse_result(key_value): + """Parse the result into a float value.""" + key, value = key_value + if key == "result": + return (key, float(value)) + return key_value + +parser_function = compose( + parse_result, + parse_rm, + parse_xyz, + parse_count, + parse_method, + lambda k_v: tuple(item.strip("\n\t ") for item in k_v), + lambda s: s.split(":")) + +def parse_input_line(line): + return tuple( + parser_function(item) for item in line if not item.startswith("------")) + +def merge_z(item): + without_z = { + key: val for key, val in item.items() if not key.startswith("z")} + return { + **without_z, + "z": item.get( + "z", + tuple(val for key, val in item.items() if key.startswith("z")))} + +def parse_input(lines): + return tuple( + merge_z(dict(item)) + for item in (parse_input_line(line) for line in lines) + if len(item) != 0) + +def parse_test_data(filename): + with open("pcor_rec_blackbox_attempt.txt", newline="\n") as fl: + input_lines = partition_by( + lambda s: s.startswith("------"), + (line.strip("\n\t ") for line in fl.readlines())) + + return parse_input(input_lines) + class TestPartialCorrelations(TestCase): """Class for testing partial correlations computation functions""" @@ -343,9 +419,9 @@ class TestPartialCorrelations(TestCase): Test that `partial_correlation_recursive` computes the appropriate correlation value. """ - for sample in parse_test_data_csv( + for sample in parse_test_data( ("tests/unit/computations/partial_correlations_test_data/" - "pcor_rec_blackbox_test.csv")): + "pcor_rec_blackbox_test.txt")): with self.subTest( xdata=sample["x"], ydata=sample["y"], zdata=sample["z"], method=sample["method"], omit_nones=sample["rm"]): @@ -353,4 +429,4 @@ class TestPartialCorrelations(TestCase): partial_correlation_recursive( sample["x"], sample["y"], sample["z"], method=sample["method"], omit_nones=sample["rm"]), - sample["result"]) + round(sample["result"], ROUND_TO)) |