snplib 1.0.0__py3-none-any.whl

parentage/tests/test_verif.py

@@ -0,0 +1,160 @@
+#!/usr/bin/env python
+# coding: utf-8
+__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
+
+from . import DIR_DATA
+from .. import Verification, isag_verif
+
+import pytest
+import pandas as pd
+
+
+@pytest.fixture
+def data() -> pd.DataFrame:
+	return pd.read_csv(DIR_DATA / "parentage_test_verf.csv", sep=" ")
+
+
+@pytest.fixture
+def obj_verification() -> Verification:
+	return Verification(isag_marks=isag_verif().markers)
+
+
+class TestVerification(object):
+
+	def test_check_on_successfully(
+		self, data: pd.DataFrame, obj_verification: Verification
+	) -> None:
+
+		assert obj_verification.check_on(
+			data=data,
+			descendant="BY000041988163",
+			parent="EE10512586",
+			snp_name_col="SNP_Name"
+		) is None
+		assert obj_verification.num_conflicts == 31
+		assert obj_verification.status == "Excluded"
+
+	def test_check_on_1(self, data: pd.DataFrame) -> None:
+		"""
+		The test checks the exception for missing token data for verification.
+		"""
+		obj_verification = Verification()
+
+		with pytest.raises(
+			ValueError, match="Error. No array of snp names to verify"
+		):
+			obj_verification.check_on(
+				data=data,
+				descendant="BY000041988163",
+				parent="EE10512586",
+				snp_name_col="SNP_Name"
+			)
+		assert obj_verification.status is None
+		assert obj_verification.num_conflicts is None
+
+	def test_check_on_2(
+		self, data: pd.DataFrame, obj_verification: Verification
+	) -> None:
+		"""
+		Exception for low call rate in both animals.
+		"""
+
+		with pytest.raises(
+			Exception, match="Calf and parent have low call rate"
+		):
+			obj_verification.check_on(
+				data=data[:-100],
+				descendant="BY000041988163",
+				parent="EE10512586",
+				snp_name_col="SNP_Name"
+			)
+		assert obj_verification.status is None
+		assert obj_verification.num_conflicts is None
+
+	def test_check_on_3(
+		self, data: pd.DataFrame, obj_verification: Verification
+	) -> None:
+		"""
+		Exception when paired call rate is below threshold.
+		"""
+
+		data.loc[228:, 'BY000041988163'] = 5
+		data.loc[239:, 'EE10512586'] = 5
+
+		with pytest.raises(
+			Exception, match="Pair call rate is low"
+		):
+			obj_verification.check_on(
+				data=data,
+				descendant="BY000041988163",
+				parent="EE10512586",
+				snp_name_col="SNP_Name"
+			)
+		assert obj_verification.status is None
+		assert obj_verification.num_conflicts is None
+
+	def test_search_parent_4(
+		self, data: pd.DataFrame, obj_verification: Verification
+	) -> None:
+		"""
+		Test if the transmitted animal names are not in the dataframe.
+		"""
+
+		# For descendant
+		with pytest.raises(KeyError):
+			obj_verification.check_on(
+				data=data,
+				descendant="BY00004198816",
+				parent="EE10512586",
+				snp_name_col="SNP_Name"
+			)
+		assert obj_verification.status is None
+		assert obj_verification.num_conflicts is None
+
+		# For parents
+		with pytest.raises(KeyError):
+			obj_verification.check_on(
+				data=data,
+				descendant="BY000041988163",
+				parent="EE105125864",
+				snp_name_col="SNP_Name"
+			)
+		assert obj_verification.status is None
+		assert obj_verification.num_conflicts is None
+
+	def test_search_parent_5(
+		self, data: pd.DataFrame, obj_verification: Verification
+	) -> None:
+		"""
+		Test when all snp data is not read - equal to 5
+		"""
+		data[["BY000041988163", "EE10512586"]] = 5
+
+		with pytest.raises(
+			Exception, match="Calf and parent have low call rate"
+		):
+			obj_verification.check_on(
+				data=data,
+				descendant="BY000041988163",
+				parent="EE10512586",
+				snp_name_col="SNP_Name"
+			)
+		assert obj_verification.status is None
+		assert obj_verification.num_conflicts is None
+
+	def test_search_parent_6(
+			self, data: pd.DataFrame, obj_verification: Verification
+	) -> None:
+		"""
+		Test when there is a complete match
+		"""
+		data[["BY000041988163", "EE10512586"]] = 2
+
+		obj_verification.check_on(
+			data=data,
+			descendant="BY000041988163",
+			parent="EE10512586",
+			snp_name_col="SNP_Name"
+		)
+		assert obj_verification.status == "Accept"
+		assert obj_verification.num_conflicts == 0