Merge pull request #14 from TheJacksonLaboratory/G3-209-add-check-thr…

…eshold-functions-to-geneweaver-core

Adding check threshold function and related tests

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-core"
-version = "0.9.0a6"
+version = "0.9.0a7"
 description = "The core of the Jax-Geneweaver Python library"
 authors = ["Jax Computational Sciences <[email protected]>"]
 readme = "README.md"

src/geneweaver/core/threshold.py

@@ -0,0 +1,42 @@
+"""A module for functions dealing with thresholding."""
+
+from typing import List
+
+from geneweaver.core.schema.score import GenesetScoreType
+
+
+def check_threshold(geneset_score: GenesetScoreType, value: float) -> bool:
+    """Check to see if a value falls within the score threshold.
+
+    :param geneset_score: The geneset score type and threshold arguments.
+    :param value: The value to check against.
+    :return: A boolean that indicates if the value falls within the range specified by
+            the threshold.
+    """
+    score_type = int(geneset_score.score_type)
+    value = float(value)
+
+    # P and Q values
+    if score_type == 1 or score_type == 2:
+        return value <= geneset_score.threshold
+
+    # Correlation and effect scores
+    elif score_type == 4 or score_type == 5:
+        return geneset_score.threshold_low <= value <= geneset_score.threshold
+
+    # Binary
+    else:
+        return value >= geneset_score.threshold
+
+
+def check_threshold_list(
+    geneset_score: GenesetScoreType, values: List[float]
+) -> List[bool]:
+    """Check to see if a list of values falls within the score threshold.
+
+    :param geneset_score: The geneset score type and threshold arguments.
+    :param values: The list of values to check against.
+    :return: A list of booleans that indicates if the value falls within the range
+            specified by the threshold.
+    """
+    return [check_threshold(geneset_score, value) for value in values]

tests/unit/threshold/__init__.py

@@ -0,0 +1 @@
+"""Tests for threshold functions."""

tests/unit/threshold/test_check_threshold.py

@@ -0,0 +1,35 @@
+"""Test the check_threshold function."""
+
+import pytest
+from geneweaver.core.schema.score import GenesetScoreType
+from geneweaver.core.threshold import check_threshold
+
+
+@pytest.mark.parametrize(
+    ("geneset_score", "value", "expected"),
+    [
+        (GenesetScoreType(score_type=1, threshold=0.05), 0.01, True),
+        (GenesetScoreType(score_type=1, threshold=0.05), 0.06, False),
+        (GenesetScoreType(score_type=2, threshold=0.05), 0.01, True),
+        (GenesetScoreType(score_type=2, threshold=0.05), 0.06, False),
+        (GenesetScoreType(score_type=3, threshold=0.05), 0.01, False),
+        (
+            GenesetScoreType(score_type=4, threshold=0.05, threshold_low=0.01),
+            0.03,
+            True,
+        ),
+        (
+            GenesetScoreType(score_type=4, threshold=0.05, threshold_low=0.01),
+            0.06,
+            False,
+        ),
+        (
+            GenesetScoreType(score_type=5, threshold=0.05, threshold_low=0.01),
+            0.03,
+            True,
+        ),
+    ],
+)
+def test_check_threshold(geneset_score, value, expected):
+    """Check each parametrized case with valid arguments."""
+    assert check_threshold(geneset_score, value) == expected

tests/unit/threshold/test_check_threshold_list.py

@@ -0,0 +1,55 @@
+"""Test the check_threshold_list function."""
+
+import pytest
+from geneweaver.core.schema.score import GenesetScoreType
+from geneweaver.core.threshold import check_threshold_list
+
+
+@pytest.mark.parametrize(
+    ("geneset_scores", "values", "expected"),
+    [
+        (GenesetScoreType(score_type=1, threshold=0.05), [0.01, 0.06], [True, False]),
+        (GenesetScoreType(score_type=2, threshold=0.05), [0.01, 0.06], [True, False]),
+        (GenesetScoreType(score_type=3, threshold=0.05), [0.01, 0.06], [False, True]),
+        (
+            GenesetScoreType(score_type=4, threshold=0.05, threshold_low=0.01),
+            [0.03, 0.06],
+            [True, False],
+        ),
+        (
+            GenesetScoreType(score_type=5, threshold=0.05, threshold_low=0.01),
+            [0.03, 0.06],
+            [True, False],
+        ),
+        (
+            GenesetScoreType(score_type="p-value", threshold=0.05),
+            [0.01, 0.06],
+            [True, False],
+        ),
+        (
+            GenesetScoreType(score_type="q-value", threshold=0.05),
+            [0.01, 0.06],
+            [True, False],
+        ),
+        (
+            GenesetScoreType(score_type="binary", threshold=0.05),
+            [0.01, 0.06],
+            [False, True],
+        ),
+        (
+            GenesetScoreType(
+                score_type="correlation", threshold=0.05, threshold_low=0.01
+            ),
+            [0.03, 0.06],
+            [True, False],
+        ),
+        (
+            GenesetScoreType(score_type="effect", threshold=0.05, threshold_low=0.01),
+            [0.03, 0.06],
+            [True, False],
+        ),
+    ],
+)
+def test_check_threshold_list(geneset_scores, values, expected):
+    """Check each parametrized case with valid arguments."""
+    assert check_threshold_list(geneset_scores, values) == expected