snplib 1.0.7__py3-none-any.whl → 1.0.9__py3-none-any.whl

snplib/statistics/tests/test_callrate.py

@@ -1,171 +0,0 @@
-#!/usr/bin/env python
-# coding: utf-8
-__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
-
-from . import DIR_DATA
-from .. import call_rate
-
-import pytest
-import numpy as np
-import pandas as pd
-
-
-@pytest.fixture
-def data_df(request) -> pd.DataFrame:
-	match request.param:
-		case "cra":
-			return pd.read_pickle(DIR_DATA / "cr/file_cra.pl")
-
-		case "crm":
-			return pd.read_pickle(DIR_DATA / "cr/file_crm.pl")
-
-
-@pytest.fixture
-def data_str() -> list[str]:
-	return ['02011015010000500', '01110152120222512']
-
-
-class TestCallRateAnimal(object):
-
-	@pytest.mark.parametrize("data_df", ["cra"], indirect=True)
-	def test_cra_datafame_dtype_obj(self, data_df: pd.DataFrame) -> None:
-		data_df.SNP = data_df.SNP.astype(str)
-		result = call_rate(data=data_df, id_col="SAMPLE_ID", snp_col="SNP")
-
-		assert isinstance(result, pd.DataFrame) and not result.empty
-		assert result.SNP.round(6).isin([0.882353, 0.882353]).all()
-
-	@pytest.mark.parametrize("data_df", ["cra"], indirect=True)
-	def test_cra_datafame_dtype_int(self, data_df: pd.DataFrame) -> None:
-		data_df.SNP = data_df.SNP.astype("int8")
-		result = call_rate(data=data_df, id_col="SAMPLE_ID", snp_col="SNP")
-
-		assert isinstance(result, pd.DataFrame) and not result.empty
-		assert result.SNP.round(6).isin([0.882353, 0.882353]).all()
-
-	@pytest.mark.parametrize("data_df", ["cra"], indirect=True)
-	def test_cra_datafame_dtype_float(self, data_df: pd.DataFrame) -> None:
-		data_df.SNP = data_df.SNP.astype("float32")
-		result = call_rate(data=data_df, id_col="SAMPLE_ID", snp_col="SNP")
-
-		assert isinstance(result, pd.DataFrame) and not result.empty
-		assert result.SNP.round(6).isin([0.882353, 0.882353]).all()
-
-	@pytest.mark.parametrize("data_df", ["cra"], indirect=True)
-	def test_cra_datafame_dtype_random_simbols(
-		self, data_df: pd.DataFrame
-	) -> None:
-		data_df.SNP = [
-			np.random.choice(["A", "C", "G", "T"])
-			for _ in range(data_df.SNP.shape[0])
-		]
-		result = call_rate(data=data_df, id_col="SAMPLE_ID", snp_col="SNP")
-
-		assert result is None
-
-	def test_cra_datafame_empty1(self) -> None:
-		with pytest.raises(KeyError):
-			call_rate(data=pd.DataFrame(), id_col="SAMPLE_ID", snp_col="SNP")
-
-	def test_cra_datafame_empty2(self) -> None:
-		result = call_rate(
-			data=pd.DataFrame(columns=["SAMPLE_ID", "SNP"]),
-			id_col="SAMPLE_ID",
-			snp_col="SNP"
-		)
-
-		assert isinstance(result, pd.DataFrame) and result.empty
-
-	@pytest.mark.parametrize("data_df", ["cra"], indirect=True)
-	def test_cra_datafame_fail(self, data_df: pd.DataFrame) -> None:
-		with pytest.raises(KeyError):
-			call_rate(data=data_df, id_col="SAMPLE_ID")
-			call_rate(data=data_df, snp_col="SNP")
-			call_rate(data=data_df)
-
-	def test_cra_str_int(self, data_str: list[str]) -> None:
-		for sequence in data_str:
-			assert call_rate(data=sequence) == 0.882353
-
-	def test_cra_str_simbols(self) -> None:
-		data_str = ['GCATGAGGTATACTCTA', 'CGCCATGCTGTATATCC']
-
-		for sequence in data_str:
-			assert call_rate(data=sequence) is None
-
-	def test_cra_str_empty(self) -> None:
-		assert call_rate(data="") is None
-
-	def test_cra_str_mixid(self) -> None:
-		assert call_rate(data="GCATGAG3G4T6A67TACTCTA") is None
-
-
-class TestCallRateMarker(object):
-
-	@pytest.mark.parametrize("data_df", ["crm"], indirect=True)
-	def test_crm_datafame_dtype_obj(self, data_df: pd.DataFrame) -> None:
-		data_df.SNP = data_df.SNP.astype(str)
-		result = call_rate(data=data_df, id_col="SNP_NAME", snp_col="SNP")
-
-		assert isinstance(result, pd.DataFrame) and not result.empty
-		assert result.SNP.round(6).isin([0.727273, 0.909091, 0.818182]).all()
-
-	@pytest.mark.parametrize("data_df", ["crm"], indirect=True)
-	def test_crm_datafame_dtype_int(self, data_df: pd.DataFrame) -> None:
-		data_df.SNP = data_df.SNP.astype("int8")
-		result = call_rate(data=data_df, id_col="SNP_NAME", snp_col="SNP")
-
-		assert isinstance(result, pd.DataFrame) and not result.empty
-		assert result.SNP.round(6).isin([0.727273, 0.909091, 0.818182]).all()
-
-	@pytest.mark.parametrize("data_df", ["crm"], indirect=True)
-	def test_crm_datafame_dtype_float(self, data_df: pd.DataFrame) -> None:
-		data_df.SNP = data_df.SNP.astype("float32")
-		result = call_rate(data=data_df, id_col="SNP_NAME", snp_col="SNP")
-
-		assert isinstance(result, pd.DataFrame) and not result.empty
-		assert result.SNP.round(6).isin([0.727273, 0.909091, 0.818182]).all()
-
-	@pytest.mark.parametrize("data_df", ["crm"], indirect=True)
-	def test_crm_datafame_dtype_random_simbols(
-		self, data_df: pd.DataFrame
-	) -> None:
-		data_df.SNP = [
-			np.random.choice(["A", "C", "G", "T"])
-			for _ in range(data_df.SNP.shape[0])
-		]
-		result = call_rate(data=data_df, id_col="SNP_NAME", snp_col="SNP")
-
-		assert result is None
-
-	def test_crm_datafame_empty1(self) -> None:
-		with pytest.raises(KeyError):
-			call_rate(data=pd.DataFrame(), id_col="SNP_NAME", snp_col="SNP")
-
-	def test_crm_datafame_empty2(self) -> None:
-		result = call_rate(
-			data=pd.DataFrame(columns=["SNP_NAME", "SNP"]),
-			id_col="SNP_NAME",
-			snp_col="SNP"
-		)
-
-		assert isinstance(result, pd.DataFrame) and result.empty
-
-	@pytest.mark.parametrize("data_df", ["crm"], indirect=True)
-	def test_crm_datafame_fail(self, data_df: pd.DataFrame) -> None:
-		with pytest.raises(KeyError):
-			call_rate(data=data_df, id_col="SNP_NAME")
-			call_rate(data=data_df, snp_col="SNP")
-			call_rate(data=data_df)
-
-	def test_crm_str_simbols(self) -> None:
-		data_str = ['GCATGAGGTATACTCTA', 'CGCCATGCTGTATATCC']
-
-		for sequence in data_str:
-			assert call_rate(data=sequence) is None
-
-	def test_crm_str_empty(self) -> None:
-		assert call_rate(data="") is None
-
-	def test_crm_str_mixid(self) -> None:
-		assert call_rate(data="GCATGAG3G4T6A67TACTCTA") is None

snplib/statistics/tests/test_freq_allele.py

@@ -1,87 +0,0 @@
-#!/usr/bin/env python
-# coding: utf-8
-__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
-
-from . import DIR_DATA
-from .. import allele_freq
-
-import pytest
-import numpy as np
-import pandas as pd
-
-
-@pytest.fixture
-def data_df() -> pd.DataFrame:
-	return pd.read_pickle(DIR_DATA / "freq/file.pl")
-	# [0.   , 0.9  , 0.889]
-
-
-def data_str() -> list[tuple]:
-	return [
-		('2212120', 0.714),
-		('02011015010000500', 0.2),
-		('01110152120222512', 0.6)
-	]
-
-
-class TestAlleleFreq(object):
-
-	def test_allele_freq_df_dtype_obj(self, data_df: pd.DataFrame) -> None:
-		data_df.SNP = data_df.SNP.astype(str)
-		result = allele_freq(data=data_df, id_col="SNP_NAME", seq_col="SNP")
-
-		assert isinstance(result, pd.DataFrame) and not result.empty
-		assert result.SNP.round(6).isin([0.000, 0.900, 0.889]).all()
-
-	def test_allele_freq_df_dtype_int(self, data_df: pd.DataFrame) -> None:
-		data_df.SNP = data_df.SNP.astype("int8")
-		result = allele_freq(data=data_df, id_col="SNP_NAME", seq_col="SNP")
-
-		assert isinstance(result, pd.DataFrame) and not result.empty
-		assert result.SNP.round(6).isin([0.000, 0.900, 0.889]).all()
-
-	def test_allele_freq_df_dtype_float(self, data_df: pd.DataFrame) -> None:
-		data_df.SNP = data_df.SNP.astype("float32")
-		result = allele_freq(data=data_df, id_col="SNP_NAME", seq_col="SNP")
-
-		assert isinstance(result, pd.DataFrame) and not result.empty
-		assert result.SNP.round(6).isin([0.000, 0.900, 0.889]).all()
-
-	def test_allele_freq_df_data_rand_simbols(
-			self, data_df: pd.DataFrame
-	) -> None:
-		data_df.SNP = [
-			np.random.choice(["A", "C", "G", "T"])
-			for _ in range(data_df.SNP.shape[0])
-		]
-		assert allele_freq(
-			data=data_df, id_col="SNP_NAME", seq_col="SNP"
-		) is None
-
-	def test_allele_freq_df_empty(self) -> None:
-		with pytest.raises(KeyError):
-			allele_freq(
-				data=pd.DataFrame(), id_col="SNP_NAME", seq_col="SNP"
-			)
-
-	def test_allele_freq_df_empty_only_columns(self) -> None:
-		result = allele_freq(
-			data=pd.DataFrame(columns=["SNP_NAME", "SNP"]),
-			id_col="SNP_NAME",
-			seq_col="SNP"
-		)
-
-		assert isinstance(result, pd.DataFrame) and result.empty
-
-	def test_allele_freq_df_raises(self, data_df: pd.DataFrame) -> None:
-		with pytest.raises(KeyError):
-			allele_freq(data=data_df, id_col="SNP_NAME")
-			allele_freq(data=data_df, seq_col="SNP")
-			allele_freq(data=data_df)
-
-	@pytest.mark.parametrize("data, obs_value", data_str())
-	def test_allele_freq_str(self, data: str, obs_value: float) -> None:
-		assert allele_freq(data=data) == obs_value
-
-	def test_allele_freq_non_type(self) -> None:
-		assert allele_freq(data=1423) is None

snplib/statistics/tests/test_freq_maf.py

@@ -1,17 +0,0 @@
-#!/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

snplib/statistics/tests/test_hwe_t.py

@@ -1,41 +0,0 @@
-#!/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)

snplib/statistics/tests/test_snphwe.py

@@ -1,41 +0,0 @@
-#!/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

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