Make sure lightmotif-py computes the right p-values

lightmotif-py/lightmotif/lib.rs

@@ -445,7 +445,7 @@ impl ScoringMatrix {
         }
     }
 
-    /// Compute the PSSM score for all positions of the given sequence.
+    /// Calculate the PSSM score for all positions of the given sequence.
     ///
     /// Returns:
     ///     `~lightmotif.StripedScores`: The PSSM scores for every position

lightmotif-py/lightmotif/tests/__init__.py

@@ -1,7 +1,8 @@
-from . import test_pipeline, test_sequence
+from . import test_pipeline, test_sequence, test_pvalue
 
 
 def load_tests(loader, suite, pattern):
     suite.addTests(loader.loadTestsFromModule(test_pipeline))
     suite.addTests(loader.loadTestsFromModule(test_sequence))
+    suite.addTests(loader.loadTestsFromModule(test_pvalue))
     return suite

lightmotif-py/lightmotif/tests/test_pvalue.py

@@ -0,0 +1,21 @@
+import unittest
+import lightmotif
+
+
+class TestMA0045(unittest.TestCase):
+
+    @classmethod
+    def setUpClass(cls):
+        cls.ma0045 = lightmotif.CountMatrix("ACTG", {
+            "A": [3, 7, 9, 3, 11, 11, 11, 3, 4, 3, 8, 8, 9, 9, 11, 2],
+            "C": [5, 0, 1, 6, 0, 0, 0, 3, 1, 4, 5, 1, 0, 5, 0, 7],
+            "T": [2, 4, 3, 1, 0, 1, 1, 6, 1, 1, 0, 1, 3, 0, 0, 5],
+            "G": [4, 3, 1, 4, 3, 2, 2, 2, 8, 6, 1, 4, 2, 0, 3, 0],
+            "N": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+        }).normalize(pseudocount=0.25).log_odds()
+
+    def test_pvalue(self):
+        self.assertAlmostEqual(self.ma0045.pvalue(8.7708), 0.00032910, places=5)
+
+    def test_score(self):
+        self.assertAlmostEqual(self.ma0045.score(0.00033), 8.756855, places=5)

lightmotif/src/pwm.rs

@@ -259,6 +259,8 @@ impl<A: Alphabet> FrequencyMatrix<A> {
 
     /// Convert to a scoring matrix using the given background frequencies.
     ///
+    /// This uses the base-2 logarithm.
+    ///
     /// # Note
     /// By convention, columns with null background frequencies receive a
     /// log-odds-ratio of [`f32::NEG_INFINITY`](https://doc.rust-lang.org/std/primitive.f32.html#associatedconstant.NEG_INFINITY).