snplib 1.1.10__py3-none-any.whl → 1.2.11__py3-none-any.whl

snplib/__init__.py

@@ -1,8 +1,8 @@
-#!/usr/bin/env python
-# coding: utf-8
-__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
-
-from .finalreport import *
-from .format import *
-from .parentage import *
-from .statistics import *
+#!/usr/bin/env python
+# coding: utf-8
+__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
+
+from .finalreport import *
+from .format import *
+from .parentage import *
+from .statistics import *

snplib/finalreport/__init__.py

@@ -1,7 +1,7 @@
-#!/usr/bin/env python
-# coding: utf-8
-__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
-
-from ._finalreport import FinalReport
-
-__all__ = ["FinalReport"]
+#!/usr/bin/env python
+# coding: utf-8
+__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
+
+from ._finalreport import FinalReport
+
+__all__ = ["FinalReport"]

snplib/finalreport/_finalreport.py

@@ -1,253 +1,305 @@
-#!/usr/bin/env python
-# coding: utf-8
-__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
-__all__ = ("FinalReport",)
-
-from pathlib import Path
-from functools import reduce
-
-import re
-
-from numpy import nan
-import pandas as pd
-
-
-class FinalReport(object):
-	""" File that contains SNP information. File processing is triggered by the
-	handle method. If values in 'SID' or 'UNIQ_KEY' were missing in the xlsx
-	conversion file, the processed data will contain NAN values.
-
-	:argument allele: A variant form of a single nucleotide polymorphism
-		(SNP), a specific polymorphic site or a whole gene detectable at
-		a locus.  Type: 'AB', 'Forward', 'Top', 'Plus', 'Design'
-	:argument sep: Delimiter to use. Default value: "\\t"
-
-	Example:
-		[Header]
-		GSGT Version	2.0.4
-		Processing Date	10/14/2021 4:02 PM
-		Content		BovineSNP50_v3_A1.bpm
-		Num SNPs	53218
-		Total SNPs	53218
-		Num Samples	3
-		Total Samples	3
-		[Data]
-		SNP Name  Sample ID  Allele1 - AB  Allele2 - AB  GC Score  GT Score
-		ABCA12	1	A	A	0.4048	0.8164
-		APAF1	1	B	B	0.9067	0.9155
-		...
-	"""
-
-	__PATTERN_HEADER = re.compile(r'(^\[Header\])')
-	__PATTERN_DATA = re.compile(r'(^\[Data\])')
-
-	def __init__(
-			self,
-			allele: str | list | None = None,
-			sep: str = "\t"
-	) -> None:
-		self._delimiter = sep
-		self._full_data = None
-
-		self.__header = {}
-		self.__snp_data = None
-		self.__allele = allele
-		self._map_rn = None
-
-	@property
-	def header(self) -> dict:
-		return self.__header
-
-	@property
-	def snp_data(self) -> pd.DataFrame | None:
-		return self.__snp_data
-
-	def handle(
-			self, file_rep: Path | str, conv_file: Path | str = None
-	) -> bool:
-		""" Processes the FinalReport.txt file. Highlights meta information
-		and data.
-
-		:param file_rep: The file FinalReport.txt or another name.
-		:param conv_file: The file that contains IDs of registration numbers
-			of animals.
-		:return: Returns true if file processing was successful, false if
-			there were errors.
-		"""
-
-		try:
-
-			if isinstance(file_rep, str):
-				file_rep = Path(file_rep)
-
-			if not file_rep.is_file() and not file_rep.exists():
-				return False
-
-			# Processing conversion file
-			if conv_file is not None:
-				if isinstance(conv_file, str):
-					conv_file = Path(conv_file)
-
-				if not conv_file.is_file() and not conv_file.exists():
-					return False
-
-				self.__convert_s_id(conv_file)
-
-			# Processing report file
-			if not self.read(file_rep):
-				return False
-
-			if self._full_data is None:
-				raise Exception("Not data in file FinalReport.txt")
-
-			self.__handler_header()
-			self.__handler_data()
-
-			if self._map_rn is not None:
-				self.__snp_data['Sample ID'] = \
-					self.__snp_data['Sample ID'].map(
-						dict(zip(self._map_rn.SID, self._map_rn.UNIQ_KEY))
-					)
-
-		except Exception as e:
-			raise e
-
-		return True
-
-	def read(self, file_rep: Path) -> bool:
-		""" Reading data from the final_report file
-
-		:param file_rep: path, pointer to the file to be read.
-		:return: Returns true if the read was successful, false if it failed.
-		"""
-		try:
-			if len(data := file_rep.read_text()) != 0:
-				self._full_data = data.strip().split("\n")
-				return True
-
-			self._full_data = None
-
-		except Exception as e:
-			return False
-
-		return True
-
-	def __handler_header(self) -> None:
-		""" Processes data from a file, selects meta-information. """
-
-		for line in self._full_data:
-			if self.__class__.__PATTERN_DATA.findall(line):
-				return
-
-			if self.__class__.__PATTERN_HEADER.findall(line):
-				continue
-
-			key = line.strip().split("\t")[0]
-			value = line.strip().split("\t")[1]
-
-			self.__header[key] = value
-
-	def __handler_data(self) -> None:
-		""" Processes data and forms an array for further processing. """
-
-		temp = 1
-		for line in self._full_data:
-			if self.__class__.__PATTERN_DATA.findall(line):
-				break
-			temp += 1
-
-		names_col = self.__sample_by_allele(
-			self._full_data[temp].split(f"{self._delimiter}")
-		)
-
-		if names_col is None:
-			raise Exception(f"Error. Allele {self.__allele} not in data.")
-
-		self.__snp_data = pd.DataFrame(
-			[
-				item_data.split(f"{self._delimiter}")
-				for item_data in self._full_data[temp + 1:]
-			],
-			columns=self._full_data[temp].split(f"{self._delimiter}")
-		)[names_col]
-
-	def __sample_by_allele(self, names: list[str]) -> list[str] | None:
-		""" Method that generates a list of field names choosing which alleles
-		to keep
-
-		:param names: List of field names in the report file.
-		:return: Returns a filtered list of fields by alleles.
-		"""
-
-		allele_templ = r'(^Allele\d\s[:-]\s{}\b)'
-
-		match self.__allele:
-			case None:
-				return names
-
-			case str():
-				allele_pattern = re.compile(
-					allele_templ.format(self.__allele)
-				)
-
-			case list() | tuple() | set():
-				allele_pattern = re.compile(
-					allele_templ.format("|".join(self.__allele))
-				)
-			case _:
-				return None
-
-		lst_allele = reduce(
-			lambda i, j: i + j,
-			[allele_pattern.findall(item) for item in names]
-		)
-
-		if len(lst_allele) == 0:
-			return None
-
-		exclude_alleles = [
-			item for item in names
-			if item.startswith("Allele") and item not in lst_allele
-		]
-
-		return list(filter(
-			lambda x: True if x not in exclude_alleles else False, names
-		))
-
-	def __convert_s_id(self, path_file: Path) -> None:
-		"""Converts sample id which is in FinalReport to animal registration
-		number.
-
-		:param path_file: xlsx file with animal numbers label
-		"""
-
-		self._map_rn = pd.read_excel(
-			path_file,
-			header=None,
-			names=['SID', 'UNIQ_KEY', 'SEX'],
-			dtype={'SID': str},
-			index_col=False
-		)
-
-		if self._map_rn.empty:
-			self._map_rn = None
-			return
-
-		self._map_rn.SID = self._map_rn.SID.str.strip()
-		self._map_rn.UNIQ_KEY = self._map_rn.UNIQ_KEY.str.strip()
-
-		if self._check_on_ru_symbols(self._map_rn.UNIQ_KEY):
-			raise Exception("Error. Unique keys contain Cyrillic alphabet.")
-
-	@staticmethod
-	def _check_on_ru_symbols(seq: pd.Series) -> bool | None:
-		""" Checial verification of the Cyrillic
-
-		:param seq: Squeezed for verification.
-		:return: Truth if there are no symbols of Cyril and there is a lie if
-			there is.
-		"""
-
-		return seq.apply(
-			lambda x: bool(re.search('[а-яА-Я]', x)) if x is not nan else x
-		).any()
+#!/usr/bin/env python
+# coding: utf-8
+__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
+__all__ = ("FinalReport",)
+
+import re
+from functools import reduce
+from pathlib import Path
+
+import pandas as pd
+from numpy import nan
+
+
+class FinalReport(object):
+	""" File that contains SNP information. File processing is triggered by the
+	handle method. If values in 'SID' or 'UNIQ_KEY' were missing in the xlsx
+	conversion file, the processed data will contain NAN values.
+
+	:param allele: A variant form of a single nucleotide polymorphism (SNP), a
+		specific polymorphic site or a whole gene detectable at a locus. Type:
+		'AB', 'Forward', 'Top', 'Plus', 'Design'.
+	:param sep: Delimiter to use. Default value: "\\t".
+	:param usecols: Selection of fields for reading. Accelerates processing
+		and reduces memory.
+	:param dtype: Data type(s) to apply to either the whole dataset or
+		individual columns. E.g., {'a': np.float64, 'b': np.int32, 'c': 'Int64'}.
+
+	Example:
+		[Header]
+		GSGT Version	2.0.4
+		Processing Date	10/14/2021 4:02 PM
+		Content		BovineSNP50_v3_A1.bpm
+		Num SNPs	53218
+		Total SNPs	53218
+		Num Samples	3
+		Total Samples	3
+		[Data]
+		SNP Name  Sample ID  Allele1 - AB  Allele2 - AB  GC Score  GT Score
+		ABCA12	1	A	A	0.4048	0.8164
+		APAF1	1	B	B	0.9067	0.9155
+		...
+	"""
+
+	__PATTERN_HEADER = re.compile(r'(^\[Header])')
+	__PATTERN_DATA = re.compile(r'(^\[Data])')
+
+	__slots__ = (
+		"_delimiter",
+		"__allele",
+		"__usecols",
+		"__dtype",
+		"__snp_data",
+		"__header",
+		"_map_rn",
+	)
+
+	def __init__(
+			self,
+			allele: str | list | None = None,
+			usecols: list[str] | None = None,
+			dtype: dict | None = None,
+			sep: str = "\t"
+	) -> None:
+		self._delimiter = sep
+		self.__allele = allele
+		self.__usecols = usecols
+		self.__dtype = dtype
+
+		# self._full_data = None
+		self.__snp_data: pd.DataFrame | None = None
+		self.__header = {}
+		self._map_rn = None
+
+	@property
+	def header(self) -> dict:
+		return self.__header
+
+	@property
+	def snp_data(self) -> pd.DataFrame | None:
+		return self.__snp_data
+
+	def handle(
+			self, file_rep: Path | str, conv_file: Path | str = None
+	) -> bool:
+		""" Processes the FinalReport.txt file. Highlights meta information
+		and data.
+
+		:param file_rep: The file FinalReport.txt or another name.
+		:param conv_file: The file that contains IDs of registration numbers
+			of animals.
+		:return: Returns true if file processing was successful, false if
+			there were errors.
+		"""
+
+		try:
+
+			if self.__allele is not None and self.__usecols is not None:
+				raise Exception("Error. Usecols is used for allele is none.")
+
+			if isinstance(file_rep, str):
+				file_rep = Path(file_rep)
+
+			if not file_rep.is_file() and not file_rep.exists():
+				return False
+
+			# Processing conversion file
+			if conv_file is not None:
+				if isinstance(conv_file, str):
+					conv_file = Path(conv_file)
+
+				if not conv_file.is_file() and not conv_file.exists():
+					return False
+
+				self.__convert_s_id(conv_file)
+
+			# # Processing report file
+			self.__handler_header(file_rep)
+			self.__handler_data(file_rep)
+
+			if not self.__snp_data.empty and self._map_rn is not None:
+				self.__snp_data['Sample ID'] = \
+					self.__snp_data['Sample ID'].map(
+						dict(zip(self._map_rn.SID, self._map_rn.UNIQ_KEY))
+					)
+
+		except Exception as e:
+			raise e
+
+		return True
+
+	def __handler_header(self, file_rep: Path) -> None:
+		""" Processes data from a file, selects meta-information.
+
+		:param file_rep: path, pointer to the file to be read.
+		"""
+
+		with open(file_rep, 'r') as file:
+
+			for line in file:
+				if self.__class__.__PATTERN_DATA.findall(line.strip()):
+					return
+
+				if self.__class__.__PATTERN_HEADER.findall(line.strip()) or\
+					len(line.strip()) == 0:
+					continue
+
+				key = line.strip().split("\t")[0]
+				value = line.strip().split("\t")[1]
+
+				self.__header[key] = value
+
+	def __handler_data(self, file_rep: Path) -> None:
+		""" Processes data and forms an array for further processing.
+
+		:param file_rep: path, pointer to the file to be read.
+		"""
+
+		with open(file_rep, 'r') as file:
+
+			# Search for the data start index and skip
+			for line in file:
+				if self.__class__.__PATTERN_DATA.findall(line.strip()):
+					break
+
+			# line column
+			orig_name_col = file.readline().strip().split(self._delimiter)
+
+			if self.__allele is None and self.__usecols is None:
+				self.__snp_data = pd.read_csv(
+					file,
+					sep=self._delimiter,
+					header=None,
+					names=orig_name_col,
+					dtype=self.__dtype,
+					low_memory=True,
+					na_filter=True
+				)
+
+				return
+
+			sub_n_col = self.__processing_columns(orig_name_col)
+			self.__snp_data = pd.read_csv(
+				file,
+				sep=self._delimiter,
+				header=None,
+				names=orig_name_col,
+				usecols=sub_n_col,
+				dtype=self.__dtype,
+				low_memory=True,
+				na_filter=True
+			)
+
+			return
+
+	def __processing_columns(self, lst_col: list[str]) -> list[str] | None:
+		""" Processing the line with all the names of the fields and the
+		sample of them.
+
+		:param lst_col: List of all fields.
+		:return: Returns a tuple with a list of names of selected fields.
+		"""
+
+		if self.__usecols is not None:
+			check_n_col = [
+				item for item in self.__usecols if item in lst_col
+			]
+
+			# Check on empty list
+			if check_n_col:
+				return self.__usecols
+
+			raise Exception(
+				f"Error. The USECOLS list contains not true fields."
+			)
+
+		# processing alleles
+		sample_n_col = self.__sample_by_allele(lst_col)
+		if sample_n_col is None:
+			raise Exception(
+				f"Error. Allele {self.__allele} not in data."
+			)
+
+		return sample_n_col
+
+	def __sample_by_allele(self, names: list[str]) -> list[str] | None:
+		""" Method that generates a list of field names choosing which alleles
+		to keep
+
+		:param names: List of field names in the report file.
+		:return: Returns a filtered list of fields by alleles.
+		"""
+
+		allele_templ = r'(^Allele\d\s[:-]\s{}\b)'
+
+		match self.__allele:
+			case None:
+				return names
+
+			case str():
+				allele_pattern = re.compile(
+					allele_templ.format(self.__allele)
+				)
+
+			case list() | tuple() | set():
+				allele_pattern = re.compile(
+					allele_templ.format("|".join(self.__allele))
+				)
+			case _:
+				return None
+
+		lst_allele = reduce(
+			lambda i, j: i + j,
+			[allele_pattern.findall(item) for item in names]
+		)
+
+		if len(lst_allele) == 0:
+			return None
+
+		exclude_alleles = [
+			item for item in names
+			if item.startswith("Allele") and item not in lst_allele
+		]
+
+		return list(filter(
+			lambda x: True if x not in exclude_alleles else False, names
+		))
+
+	def __convert_s_id(self, path_file: Path) -> None:
+		"""Converts sample id which is in FinalReport to animal registration
+		number.
+
+		:param path_file: xlsx file with animal numbers label
+		"""
+
+		self._map_rn = pd.read_excel(
+			path_file,
+			header=None,
+			names=['SID', 'UNIQ_KEY', 'SEX'],
+			index_col=False
+		)
+
+		if self._map_rn.empty:
+			self._map_rn = None
+			return
+
+		if self._map_rn.SID.dtypes == "O":
+			self._map_rn.SID = self._map_rn.SID.str.strip()
+
+		self._map_rn.UNIQ_KEY = self._map_rn.UNIQ_KEY.str.strip()
+
+		if self._check_on_ru_symbols(self._map_rn.UNIQ_KEY):
+			raise Exception("Error. Unique keys contain Cyrillic alphabet.")
+
+	@staticmethod
+	def _check_on_ru_symbols(seq: pd.Series) -> bool | None:
+		""" Checial verification of the Cyrillic
+
+		:param seq: Squeezed for verification.
+		:return: Truth if there are no symbols of Cyril and there is a lie if
+			there is.
+		"""
+
+		return seq.apply(
+			lambda x: bool(re.search('[а-яА-Я]', x)) if x is not nan else x
+		).any()

snplib/format/__init__.py

@@ -1,19 +1,19 @@
-#!/usr/bin/env python
-# coding: utf-8
-__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
-
-from ._snp import Snp
-from ._plink import (
-	make_map,
-	make_ped,
-	make_lgen,
-	make_fam
-)
-
-__all__ = [
-	"Snp",
-	"make_map",
-	"make_ped",
-	"make_fam",
-	"make_lgen"
-]
+#!/usr/bin/env python
+# coding: utf-8
+__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
+
+from ._snp import Snp
+from ._plink import (
+	make_map,
+	make_ped,
+	make_lgen,
+	make_fam
+)
+
+__all__ = [
+	"Snp",
+	"make_map",
+	"make_ped",
+	"make_fam",
+	"make_lgen"
+]

snplib/format/__settings.py

@@ -1,7 +1,7 @@
-#!/usr/bin/env python
-# coding: utf-8
-__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
-
-FIELDS_ILLUMIN = ['SNP Name', 'Sample ID', 'Allele1 - AB', 'Allele2 - AB']
-RENAME_FIELDS = ['SNP_NAME', 'SAMPLE_ID', 'ALLELE1', 'ALLELE2']
-MAP_FIELDS = dict(zip(FIELDS_ILLUMIN, RENAME_FIELDS))
+#!/usr/bin/env python
+# coding: utf-8
+__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
+
+FIELDS_ILLUMIN = ['SNP Name', 'Sample ID', 'Allele1 - AB', 'Allele2 - AB']
+RENAME_FIELDS = ['SNP_NAME', 'SAMPLE_ID', 'ALLELE1', 'ALLELE2']
+MAP_FIELDS = dict(zip(FIELDS_ILLUMIN, RENAME_FIELDS))