snplib 1.0.7__py3-none-any.whl → 1.0.8__py3-none-any.whl

{snplib-1.0.7.dist-info → snplib-1.0.8.dist-info}/METADATA

@@ -1,97 +1,80 @@
-Metadata-Version: 2.2
-Name: snplib
-Version: 1.0.7
-Summary: Snptools is a tool for Single Nucleotide Polymorphism (SNP) data processing
-Author-email: Igor <igor.loschinin@gmail.com>
-License: GNU
-Project-URL: Homepage, https://github.com/IgorekLoschinin/snptools
-Classifier: Programming Language :: Python :: 3
-Classifier: Operating System :: OS Independent
-Requires-Python: >=3.10
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: numpy>=1.26.1
-Requires-Dist: pandas>=2.1.1
-Requires-Dist: six>=1.16.0
-Requires-Dist: swifter>=1.4.0
-Requires-Dist: xlrd>=2.0.1
-Requires-Dist: XlsxWriter>=3.1.9
-Requires-Dist: openpyxl>=3.1.2
-Requires-Dist: pydantic>=2.4.2
-Requires-Dist: pytest>=7.4.2
-
-# snptools
-
-**Snptools** is a tool for SNP (Single Nucleotide Polymorphism) data processing, 
-parentage calculation and call rate estimation.
-
-## Introduction
-
-SNP (Single Nucleotide Polymorphism) represent genetic variations, that can 
-be used to analyze genetic data. SNPTools provides a set of tools for working 
-with SNP data, including the following capabilities:
-
-- SNP data processing - FinalReport.
-- Parentage Verification and Parentage Discovery Based on SNP Genotypes (ICAR). 
-- Call rate estimation (percentage of missing data).
-- Processing and preparation of data in plink formats.
-
-## Installation
-
-To install SNPTools, follow the steps below:
-
-1. Clone the repository into your project directory:
-   ```
-   git clone https://github.com/yourusername/snpTools.git
-   ```
-2. Set dependencies:
-   ```
-   pip install -r requirements.txt
-   ```
-3. Use SNPTools:
-   ```
-   import snptools
-   ```
-
-or 
-
-You can install snptools via pip from [PyPI](https://pypi.org/project/snplib/):
-```
-pip install snplib
-```
-
-
-## Usage
-Snptools provides commands for a variety of operations. Here are examples of 
-usage:
-
-#### SNP data processing:
-```
-from snptools import FinalReport
-```
-
-#### Computation of parentage:
-```
-from snptools import Discovery, Verification
-```
-
-#### Preparation format files:
-```
-from snptools import (
-   Snp, make_fam, make_ped, make_lgen, make_map
-)
-```
-
-#### Stat:
-```
-from snptools import (
-   hwe, hwe_test, call_rate, allele_freq, minor_allele_freq
-)
-```
-
-## Documentation
-Detailed documentation on how to use SNPTools is available see the [docs](./docs/_build/index.html).
-
-## License
-This project is licensed under the GNU General Public License - see the 
-LICENSE file for details.
+Metadata-Version: 2.2
+Name: snplib
+Version: 1.0.8
+Summary: Snptools is a tool for Single Nucleotide Polymorphism (SNP) data processing
+Author-email: Igor <igor.loschinin@gmail.com>
+License: GNU
+Project-URL: Homepage, https://github.com/IgorekLoschinin/snptools
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.26.1
+Requires-Dist: pandas>=2.1.1
+Requires-Dist: six>=1.16.0
+Requires-Dist: swifter>=1.4.0
+Requires-Dist: xlrd>=2.0.1
+Requires-Dist: XlsxWriter>=3.1.9
+Requires-Dist: openpyxl>=3.1.2
+Requires-Dist: pydantic>=2.4.2
+
+# snptools
+<p align="center">
+  <img width="150" height="150" src="./iconlib.png">
+</p>
+
+**Snptools** is a tool for SNP (Single Nucleotide Polymorphism) data processing, 
+parentage calculation and call rate estimation.
+
+## Introduction
+
+SNP (Single Nucleotide Polymorphism) represent genetic variations, that can 
+be used to analyze genetic data. SNPTools provides a set of tools for working 
+with SNP data, including the following capabilities:
+
+- SNP data processing - FinalReport.
+- Parentage Verification and Parentage Discovery Based on SNP Genotypes (ICAR). 
+- Call rate estimation (percentage of missing data).
+- Processing and preparation of data in plink formats.
+
+## Installation
+You can install snptools via pip from [PyPI](https://pypi.org/project/snplib/):
+```
+pip install snplib
+```
+
+## Usage
+Snptools provides commands for a variety of operations. Here are examples of 
+usage:
+
+#### SNP data processing:
+```
+from snplib import FinalReport
+```
+
+#### Computation of parentage:
+```
+from snplib import Discovery, Verification
+```
+
+#### Preparation format files:
+```
+from snplib import (
+   Snp, make_fam, make_ped, make_lgen, make_map
+)
+```
+
+#### Stat:
+```
+from snplib import (
+   hwe, hwe_test, call_rate, allele_freq, minor_allele_freq
+)
+```
+
+## Documentation
+Detailed documentation on how to use SNPTools is available see the [docs](./docs/_build/index.html).
+
+## License
+This project is licensed under the GNU General Public License - see the 
+LICENSE file for details.

snplib-1.0.8.dist-info/RECORD

@@ -0,0 +1,22 @@
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+snplib/finalreport/__init__.py,sha256=Yk49x8t-STIfsdP6QLMtaGm1gTj_n-XS8kchPguvW1g,161
+snplib/finalreport/_finalreport.py,sha256=el_d8MVmpic3wKCRJ-J52VZYSmMuNSf4p_tmPkgh0Z0,5876
+snplib/format/__init__.py,sha256=3W_l_sP1u9HV3HWwnsJxPGw9anrVknstqLaJmWQaG0k,261
+snplib/format/__settings.py,sha256=kyAVZ4tiU61sNr3jQhjXbLXRyBA3pjFfCw3fOfSkY14,289
+snplib/format/_plink.py,sha256=Z09IOPACOt3n8CKEVRkE4tLT16I8e_6ZoMaWRxSImrA,10529
+snplib/format/_snp.py,sha256=oI-V4-_w28aX-VxoimywLDDnX6owhdjLbqt9a54_ouU,3172
+snplib/parentage/__init__.py,sha256=bN3mWTxmaFQ1qzRtyMLaAoxfomz6jnoWa-kmnJ9q_fE,280
+snplib/parentage/_discov.py,sha256=qGlNzpl4xKOWRr6-fi1osylzizgiPO8vCus8VE56nec,3180
+snplib/parentage/_isagmark.py,sha256=0xi9YhuIpU7zf16HnWw1XIkcQLk4rTNeAeCE-5p9hQE,356
+snplib/parentage/_verif.py,sha256=VbX46dC4tl4Qeuw65aRg1s6hSn0FI25Hy9-3U_jxmrg,3019
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+snplib/statistics/__init__.py,sha256=XJFU7mEwAJJ2M187jEkO8rFNYKoxF-g9KF_stS7eFFw,302
+snplib/statistics/_callrate.py,sha256=ghB1EXT5JLQeIEIzh8LjWpqAnhCtCOk6l5ecNMLtQa0,1865
+snplib/statistics/_freq.py,sha256=ZPZBZM3xq9EseOxuMzRVvzkjjFfaaA4ZvF7XI8ctON0,1623
+snplib/statistics/_snphwe.py,sha256=KcoRGwovMCc53-GJ8VfYs_3ZEHObgt8B0EvrW5nFnmM,3353
+snplib-1.0.8.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+snplib-1.0.8.dist-info/METADATA,sha256=Imm2fupAtiH61erPCanyjqNv50ssw0nLTEDwHJ92KE0,2165
+snplib-1.0.8.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+snplib-1.0.8.dist-info/top_level.txt,sha256=CGCrLXuCSyXPCTwMFQjPxQR7b93FFFft56sAPPun_2g,7
+snplib-1.0.8.dist-info/RECORD,,

snplib/finalreport/tests/__init__.py

@@ -1,7 +0,0 @@
-#!/usr/bin/env python
-# coding: utf-8
-__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
-
-from pathlib import Path
-
-DIR_FILES = Path(__file__).parent.joinpath("files")

snplib/finalreport/tests/test_finalreport.py

@@ -1,215 +0,0 @@
-#!/usr/bin/env python
-# coding: utf-8
-__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
-
-
-from . import DIR_FILES
-from .._finalreport import FinalReport
-
-import pytest
-
-
-@pytest.fixture
-def report(request) -> FinalReport:
-	return FinalReport(allele=request.param)
-
-
-class TestFinalReport(object):
-
-	@pytest.mark.parametrize("report", [None], indirect=True)
-	def test_handle_1(self, report: FinalReport) -> None:
-		""" If both files do not exist """
-
-		assert not report.handle(
-			DIR_FILES / "fr/f.txt", DIR_FILES / "fr/f.xlsx",
-		)
-
-	@pytest.mark.parametrize("report", [None], indirect=True)
-	def test_handle_2(self, report: FinalReport) -> None:
-		""" If the file to convert does not exist """
-
-		assert not report.handle(
-			DIR_FILES / "fr/file1.txt", DIR_FILES / "fr/f.xlsx",
-		)
-
-	@pytest.mark.parametrize("report", [None], indirect=True)
-	def test_handle_3(self, report: FinalReport) -> None:
-		""" If the data does not contain header data """
-
-		report.handle(
-			DIR_FILES / "fr/file2.txt", DIR_FILES / "fr/file2.xlsx",
-		)
-
-		assert len(report.header) == 0 and not report.snp_data.empty
-
-	@pytest.mark.parametrize("report", [None], indirect=True)
-	def test_handle_4(self, report: FinalReport) -> None:
-		""" If the file contains only header and field names """
-
-		report.handle(
-			DIR_FILES / "fr/file3.txt", DIR_FILES / "fr/file3.xlsx",
-		)
-
-		assert report.snp_data is not None and report.snp_data.empty
-
-	@pytest.mark.parametrize("report", [None], indirect=True)
-	def test_handle_5(self, report: FinalReport) -> None:
-		""" If the data file is empty """
-
-		with pytest.raises(
-				Exception, match="Not data in file FinalReport.txt"
-		):
-			report.handle(
-				DIR_FILES / "fr/file5.txt", DIR_FILES / "fr/file5.xlsx",
-			)
-
-		assert report.snp_data is None
-
-	@pytest.mark.parametrize("report", [None], indirect=True)
-	def test_handle_6(self, report: FinalReport) -> None:
-		""" If the conversion file is empty """
-
-		assert report.handle(
-			DIR_FILES / "fr/file6.txt", DIR_FILES / "fr/file6.xlsx",
-		)
-
-		assert not report.snp_data.empty
-		assert len(report.header) != 0
-
-	@pytest.mark.parametrize("report", [None], indirect=True)
-	def test_handle_7(self, report: FinalReport) -> None:
-		""" If the data file is not needed to convert ID name """
-
-		report.handle(DIR_FILES / "fr/file4.txt", None)
-
-		assert not report.snp_data.empty
-		assert len(report.header) != 0
-
-	@pytest.mark.parametrize("report", [None], indirect=True)
-	def test_handle_8(self, report: FinalReport) -> None:
-		""" If files exist """
-
-		assert report.handle(
-			DIR_FILES / "fr/file1.txt", DIR_FILES / "fr/file1.xlsx",
-		)
-
-	@pytest.mark.parametrize("report", [None], indirect=True)
-	def test_allele_none(self, report: FinalReport) -> None:
-		report.handle(DIR_FILES / "fr/file4.txt", None)
-
-		_fields = [
-			'SNP Name', 'Sample ID', 'Allele1 - Forward', 'Allele2 - Forward',
-			'Allele1 - Top', 'Allele2 - Top', 'Allele1 - AB', 'Allele2 - AB',
-			'GC Score', 'X', 'Y'
-		]
-
-		assert report.snp_data.columns.difference(_fields).empty
-
-	@pytest.mark.parametrize("report", ["AB"], indirect=True)
-	def test_sample_allele_ab(self, report: FinalReport) -> None:
-		report.handle(DIR_FILES / "fr/file4.txt", None)
-
-		_fields = [
-			'SNP Name', 'Sample ID', 'Allele1 - AB', 'Allele2 - AB',
-			'GC Score', 'X', 'Y'
-		]
-
-		assert report.snp_data.columns.difference(_fields).empty
-
-	@pytest.mark.parametrize("report", ["Forward"], indirect=True)
-	def test_sample_allele_forward(self, report: FinalReport) -> None:
-		report.handle(DIR_FILES / "fr/file4.txt", None)
-
-		_fields = [
-			'SNP Name', 'Sample ID', 'Allele1 - Forward', 'Allele2 - Forward',
-			'GC Score', 'X', 'Y'
-		]
-
-		assert report.snp_data.columns.difference(_fields).empty
-
-	@pytest.mark.parametrize("report", ["Top"], indirect=True)
-	def test_sample_allele_top(self, report: FinalReport) -> None:
-		report.handle(DIR_FILES / "fr/file4.txt", None)
-
-		_fields = [
-			'SNP Name', 'Sample ID', 'Allele1 - Top', 'Allele2 - Top',
-			'GC Score', 'X', 'Y'
-		]
-
-		assert report.snp_data.columns.difference(_fields).empty
-
-	@pytest.mark.parametrize("report", [["AB", "Top"]], indirect=True)
-	def test_sample_allele_list1(self, report: FinalReport) -> None:
-		report.handle(DIR_FILES / "fr/file4.txt", None)
-
-		_fields = [
-			'SNP Name', 'Sample ID', 'Allele1 - Top', 'Allele2 - Top',
-			'Allele1 - AB', 'Allele2 - AB', 'GC Score', 'X', 'Y'
-		]
-
-		assert report.snp_data.columns.difference(_fields).empty
-
-	@pytest.mark.parametrize("report", [["AB"]], indirect=True)
-	def test_sample_allele_list2(self, report: FinalReport) -> None:
-		report.handle(DIR_FILES / "fr/file4.txt", None)
-
-		_fields = [
-			'SNP Name', 'Sample ID', 'Allele1 - AB', 'Allele2 - AB',
-			'GC Score', 'X', 'Y'
-		]
-
-		assert report.snp_data.columns.difference(_fields).empty
-
-	@pytest.mark.parametrize("report", [("AB", "Top")], indirect=True)
-	def test_sample_allele_tuple(self, report: FinalReport) -> None:
-		report.handle(DIR_FILES / "fr/file4.txt", None)
-
-		_fields = [
-			'SNP Name', 'Sample ID', 'Allele1 - Top', 'Allele2 - Top',
-			'Allele1 - AB', 'Allele2 - AB', 'GC Score', 'X', 'Y'
-		]
-
-		assert report.snp_data.columns.difference(_fields).empty
-
-	@pytest.mark.parametrize("report", [{"AB", "Top"}], indirect=True)
-	def test_sample_allele_set(self, report: FinalReport) -> None:
-		report.handle(DIR_FILES / "fr/file4.txt", None)
-
-		_fields = [
-			'SNP Name', 'Sample ID', 'Allele1 - Top', 'Allele2 - Top',
-			'Allele1 - AB', 'Allele2 - AB', 'GC Score', 'X', 'Y'
-		]
-
-		assert report.snp_data.columns.difference(_fields).empty
-
-	@pytest.mark.parametrize("report", ["GG"], indirect=True)
-	def test_sample_allele_not_exist(self, report: FinalReport) -> None:
-
-		with pytest.raises(
-				Exception, match="Error. Allele GG not in data."
-		):
-			report.handle(DIR_FILES / "fr/file4.txt", None)
-
-	@pytest.mark.parametrize("report", ["AB"], indirect=True)
-	def test_7(self, report: FinalReport) -> None:
-
-		with pytest.raises(
-			Exception, match="Error. Unique keys contain Cyrillic alphabet."
-		):
-			report.handle(
-				DIR_FILES / "fr/file7.txt", DIR_FILES / "fr/file7.xlsx"
-			)
-
-	# 	assert not report.snp_data.empty
-	#
-	# @pytest.mark.parametrize("report", ["AB"], indirect=True)
-	# def test_8(self, report: FinalReport) -> None:
-	# 	...
-	#
-	# @pytest.mark.parametrize("report", ["AB"], indirect=True)
-	# def test_9(self, report: FinalReport) -> None:
-	# 	...
-	#
-	# @pytest.mark.parametrize("report", ["AB"], indirect=True)
-	# def test_10(self, report: FinalReport) -> None:
-	# 	...

snplib/format/tests/__init__.py

@@ -1,7 +0,0 @@
-#!/usr/bin/env python
-# coding: utf-8
-__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
-
-from pathlib import Path
-
-DIR_FILES = Path(__file__).parent.joinpath("files")

snplib/format/tests/test_plink_fam.py

@@ -1,121 +0,0 @@
-#!/usr/bin/env python
-# coding: utf-8
-__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
-
-from . import DIR_FILES
-from .. import make_fam
-
-import pytest
-import pandas as pd
-
-
-@pytest.fixture
-def data_fam(request) -> pd.DataFrame | None:
-	return pd.read_pickle(DIR_FILES / f"fplink/fam/{request.param}")
-
-
-class TestPlinkFormatPed(object):
-
-	@pytest.mark.parametrize("data_fam", ["file.pl"], indirect=True)
-	def test_fam_true(self, data_fam: pd.DataFrame) -> None:
-		assert not make_fam(
-			data_fam,
-			"SAMPLE_ID",
-			"SAMPLE_ID"
-		).empty
-
-		assert not make_fam(
-			data_fam,
-			"SAMPLE_ID",
-			"SAMPLE_ID"
-		).empty
-
-	def test_fam_empty(self) -> None:
-		assert make_fam(
-			pd.DataFrame(columns=["SAMPLE_ID", "SNP"]),
-			"SAMPLE_ID",
-		).empty
-
-		assert make_fam(
-			pd.DataFrame(columns=["SAMPLE_ID", "SNP"]),
-			"SAMPLE_ID",
-			"SAMPLE_ID",
-		).empty
-
-	@pytest.mark.parametrize("data_fam", ["file.pl"], indirect=True)
-	def test_fam_raise_columns(self, data_fam: pd.DataFrame) -> None:
-		# SID_COL
-		with pytest.raises(
-				KeyError, match="Data has not in name columns SAMPLE_ID1!"
-		):
-			make_fam(
-				data_fam,
-				"SAMPLE_ID1",
-				"SAMPLE_ID",
-			)
-
-		# FID_COL
-		with pytest.raises(
-				KeyError, match="Data has not in name columns SAMPLE_ID1!"
-		):
-			make_fam(
-				data_fam,
-				"SAMPLE_ID",
-				"SAMPLE_ID1"
-			)
-
-	@pytest.mark.parametrize("data_fam", ["file2.pl"], indirect=True)
-	def test_fam_raises_underscope_sid(self, data_fam: pd.DataFrame) -> None:
-
-		# SID_COL
-		with pytest.raises(
-				Exception,
-				match="Replace in 'Sample ID' columns '_' on another a simbols"
-		):
-			make_fam(
-				data_fam,
-				"SAMPLE_ID",
-				"SAMPLE_ID"
-			)
-
-	@pytest.mark.parametrize("data_fam", ["file3.pl"], indirect=True)
-	def test_fam_raises_underscope_fid(self, data_fam: pd.DataFrame) -> None:
-
-		# FID_COL
-		with pytest.raises(
-				Exception,
-				match="Replace in 'Family ID' columns '_' on another a simbols"
-		):
-			make_fam(
-				data_fam,
-				"SAMPLE_ID",
-				"FAMILY_ID"
-			)
-
-	@pytest.mark.parametrize("data_fam", ["file4.pl"], indirect=True)
-	def test_fam_check_data(self, data_fam: pd.DataFrame) -> None:
-		res = make_fam(
-			data_fam,
-			"SAMPLE_ID",
-			"FAMILY_ID",
-			father_col="father",
-			mother_col="mother",
-			sex_col="sex",
-			pheno_col="pheno"
-		)
-
-		res2 = make_fam(
-			data_fam,
-			"SAMPLE_ID",
-			"FAMILY_ID",
-		)
-
-		assert all(res.father.values == list('1234'))
-		assert all(res.mother.values == list('5678'))
-		assert all(res.sex.values == list('1210'))
-		assert all(res.pheno.values == ['12', '13', '14', '15'])
-
-		assert all(res2.father.values == list('0000'))
-		assert all(res2.mother.values == list('0000'))
-		assert all(res2.sex.values == list('0000'))
-		assert all(res2.pheno.values == ['-9', '-9', '-9', '-9'])

snplib/format/tests/test_plink_lgen.py

@@ -1,106 +0,0 @@
-#!/usr/bin/env python
-# coding: utf-8
-__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
-
-from . import DIR_FILES
-from .. import make_lgen
-
-import pytest
-import pandas as pd
-
-
-@pytest.fixture
-def data_lgen(request) -> pd.DataFrame:
-	return pd.read_pickle(DIR_FILES / f"fplink/lgen/{request.param}")
-
-
-class TestPlinkFormatLgen(object):
-
-	@pytest.mark.parametrize("data_lgen", ["file.pl"], indirect=True)
-	def test_lgen_true(self, data_lgen: pd.DataFrame) -> None:
-		assert not make_lgen(
-			data_lgen,
-			"Sample ID",
-			"SNP Name",
-			["Allele1 - AB", "Allele2 - AB"]
-		).empty
-
-	def test_lgen_empty(self) -> None:
-		assert make_lgen(
-			pd.DataFrame(columns=[
-				"Sample ID", "SNP Name", "Allele1 - AB", "Allele2 - AB"
-			]),
-			"Sample ID",
-			"SNP Name",
-			["Allele1 - AB", "Allele2 - AB"]
-		).empty
-
-	@pytest.mark.parametrize("data_lgen", ["file.pl"], indirect=True)
-	def test_lgen_raise_columns(self, data_lgen: pd.DataFrame) -> None:
-
-		with pytest.raises(
-			Exception,
-			match="Replace in 'Sample ID' columns '_' on another a simbols"
-		):
-			res1 = data_lgen.copy(deep=True)
-			res1["Sample ID"] = res1["Sample ID"] + "_"
-
-			make_lgen(
-				res1,
-				"Sample ID",
-				"SNP Name",
-				["Allele1 - AB", "Allele2 - AB"]
-			)
-
-		with pytest.raises(
-			Exception,
-			match="Replace in 'Family ID' columns '_' on another a simbols"
-		):
-			res1 = data_lgen.copy(deep=True)
-			res1["Family ID"] = res1["Sample ID"] + "_"
-
-			make_lgen(
-				res1,
-				"Sample ID",
-				"SNP Name",
-				["Allele1 - AB", "Allele2 - AB"],
-				fid_col="Family ID"
-			)
-
-		# SID
-		with pytest.raises(KeyError):
-			make_lgen(
-				data_lgen,
-				"Sample ID1",
-				"SNP Name",
-				["Allele1 - AB", "Allele2 - AB"],
-				fid_col="Family ID"
-			)
-
-		# FID_COL
-		with pytest.raises(KeyError):
-			make_lgen(
-				data_lgen,
-				"Sample ID",
-				"SNP Name",
-				["Allele1 - AB", "Allele2 - AB"],
-				fid_col="Family ID"
-			)
-
-		# SNP name
-		with pytest.raises(KeyError):
-			make_lgen(
-				data_lgen,
-				"Sample ID",
-				"SNP Name1",
-				["Allele1 - AB", "Allele2 - AB"]
-			)
-
-		# Alleles
-		with pytest.raises(KeyError):
-			make_lgen(
-				data_lgen,
-				"Sample ID",
-				"SNP Name",
-				["Allele1 - AB1", "Allele2 - AB1"]
-			)