snplib 1.0.0__py3-none-any.whl

statistics/tests/test_freq_maf.py

@@ -0,0 +1,17 @@
+#!/usr/bin/env python
+# coding: utf-8
+__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
+
+from .. import minor_allele_freq as maf
+
+import pytest
+
+
+class TestMinorAlleleFreq(object):
+
+	@pytest.mark.parametrize("value, res", [
+		(0.0, 0.0), (0.9, 0.1), (0.889, 0.111),
+		(0.714, 0.286), (0.22, 0.22), (0.45, 0.45), (0.6, 0.4)
+	])
+	def test_minor_allele_freq(self, value: float, res: float) -> None:
+		assert maf(value) == res

statistics/tests/test_hwe_t.py

@@ -0,0 +1,41 @@
+#!/usr/bin/env python
+# coding: utf-8
+__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
+
+from .. import hwe_test
+
+import pytest
+import pandas as pd
+
+
+class TestHWE(object):
+
+	@pytest.mark.parametrize(
+		"seq, freq",
+		[
+			('2212120', 0.714),
+			('02011015010000500', 0.2),
+			('01110152120222512', 0.6),
+			('00005005005', 0.0),
+			('22521212222', 0.9),
+			('52221521222', 0.889)
+		]
+	)
+	def test_hweT_true(self, seq: str, freq: float) -> None:
+		"""
+		 check snphwe gives expected p-values
+		"""
+
+		_seq_snp = pd.Series(list(map(int, seq)))
+
+		assert hwe_test(_seq_snp, freq)
+
+	@pytest.mark.parametrize("seq, freq", [('000000000102', 0.125)])
+	def test_hweT_false(self, seq: str, freq: float) -> None:
+		"""
+		 check snphwe gives expected p-values
+		"""
+
+		_seq_snp = pd.Series(list(map(int, seq)))
+
+		assert not hwe_test(_seq_snp, freq)

statistics/tests/test_snphwe.py

@@ -0,0 +1,41 @@
+#!/usr/bin/env python
+# coding: utf-8
+__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
+
+from .. import hwe
+
+import pytest
+
+
+class TestHWE(object):
+
+	def test_snphwe(self) -> None:
+		"""
+		 check snphwe gives expected p-values
+		"""
+		assert hwe(500, 10, 5000) == 0.6515718999145375
+		assert hwe(1000, 20, 5000) == 1.2659849194317374e-05
+
+	def test_snphwe_odd_inputs(self) -> None:
+		"""
+		check snphwe with odd inputs
+		"""
+		# should raise errors with odd inputs
+
+		with pytest.raises(ValueError, match="snphwe: zero genotypes"):
+			hwe(0, 0, 0)
+
+		with pytest.raises(ValueError, match="snphwe: negative allele count"):
+			hwe(-5, 10, 1000)
+
+	def test_snphwe_large_input(self) -> None:
+		"""
+		check snphwe doesn't give errors with large sample sizes
+		"""
+		assert hwe(200000, 200000, 200000) == 0.0
+
+	def test_snphwe_uncertain_genotypes(self) -> None:
+		"""
+		check uncertain genotypes give correct p-values
+		"""
+		assert hwe(4989.99999, 494999.999, 9.9999999) == 0.5702231983054381