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

snplib/format/_snp.py

@@ -1,113 +1,113 @@
-# !/usr/bin/env python
-# coding: utf-8
-
-__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
-
-from pathlib import Path
-from .__settings import FIELDS_ILLUMIN, MAP_FIELDS
-
-import pandas as pd
-
-
-class Snp(object):
-	""" The process of converting genomic map data - FinalReport.txt obtained
-	from Illumin. Recoding allele data into quantitative data, saving in the
-	format necessary for calculating gblup on blupf90.
-
-	:argument fmt: Data format to use snp in plink and blupf90. Default
-		value "uga". """
-
-	_ALLELE_CODE = {
-		'AA': 0, 'AB': 1, 'BA': 1, 'BB': 2, '--': 5
-	}
-
-	_FIELDS = ['SNP_NAME', 'SAMPLE_ID', 'SNP']
-	_F_DTYPE = dict(zip(_FIELDS, (str for _ in range(len(_FIELDS)))))
-
-	def __init__(self, fmt: str | None = "uga") -> None:
-		self._format_data = fmt
-		self.__data_snp = None
-
-	@property
-	def data(self) -> pd.DataFrame | None:
-		return self.__data_snp
-
-	def process(self, data: pd.DataFrame) -> None:
-		""" Data processing and formatting. Calculation of statistical
-		information
-
-		:param data: Data from FinalReport file. Example:
-			SNP Name  Sample ID  Allele1 - AB  Allele2 - AB  GC Score  GT Score
-			ABCA12	14814	A	A	0.4048	0.8164
-			ARS-BFGL-BAC-13031	14814	B	B	0.9083	0.8712
-			ARS-BFGL-BAC-13039	14814	A	A	0.9005	0.9096
-			ARS-BFGL-BAC-13049	14814	A	B	0.9295	0.8926
-
-		:return: Returns true if the data was formatted successfully and
-			statistical information was calculated, false if an error.
-		"""
-
-		if not all(list(map(lambda x: x in data.columns, FIELDS_ILLUMIN))):
-			raise KeyError(
-				'The name of the fields does not match the finalreport.txt '
-				'file from Illumina'
-			)
-
-		self.__data_snp = data.rename(columns=MAP_FIELDS)
-		self.__data_snp['SNP'] = \
-			self.__data_snp[['ALLELE1', 'ALLELE2']].\
-			sum(axis=1).\
-			map(Snp._ALLELE_CODE)
-
-		self.__data_snp = self.__data_snp[Snp._FIELDS].astype(Snp._F_DTYPE)
-
-		if self._format_data is not None and self._format_data == "uga":
-			self.__data_snp = self._format_uga(
-				self.__data_snp[['SAMPLE_ID', 'SNP']]
-			)
-
-	@staticmethod
-	def _format_uga(data: pd.DataFrame) -> pd.DataFrame:
-		""" Data format to use snp in plink and blupf90. """
-
-		return data.groupby(by='SAMPLE_ID').sum().reset_index()
-
-	def to_file(self, file_path: str | Path) -> None:
-		""" Saving data to a file.
-
-		:param file_path: Path to file
-		"""
-
-		if isinstance(file_path, str):
-			file_path = Path(file_path)
-
-		if self._format_data is not None and self._format_data == "uga":
-
-			max_len = self.__data_snp["SAMPLE_ID"].str.len().max()
-
-			self.__data_snp.\
-				apply(
-					lambda x: " ".join([
-						self._add_space(x.iloc[0], max_len), x.iloc[1]
-					]),
-					axis=1
-				).\
-				to_csv(file_path, index=False, header=False)
-
-			self.__data_snp["SAMPLE_ID"] = \
-				self.__data_snp["SAMPLE_ID"].str.strip()
-
-			return None
-
-		self.__data_snp.to_csv(file_path, sep=" ", index=False)
-
-	@staticmethod
-	def _add_space(value: str, max_len: int) -> str:
-		""" Adding spaces up to the maximum length of the value in the
-		sample_id data.
-
-		:param value: Sample_id value
-		:param max_len: Max len sample_id value
-		:return: Return replacing value
-		"""
-		return "".join([value, " " * (max_len - len(value))])
+# !/usr/bin/env python
+# coding: utf-8
+
+__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
+
+from pathlib import Path
+from .__settings import FIELDS_ILLUMIN, MAP_FIELDS
+
+import pandas as pd
+
+
+class Snp(object):
+	""" The process of converting genomic map data - FinalReport.txt obtained
+	from Illumin. Recoding allele data into quantitative data, saving in the
+	format necessary for calculating gblup on blupf90.
+
+	:argument fmt: Data format to use snp in plink and blupf90. Default
+		value "uga". """
+
+	_ALLELE_CODE = {
+		'AA': 0, 'AB': 1, 'BA': 1, 'BB': 2, '--': 5
+	}
+
+	_FIELDS = ['SNP_NAME', 'SAMPLE_ID', 'SNP']
+	_F_DTYPE = dict(zip(_FIELDS, (str for _ in range(len(_FIELDS)))))
+
+	def __init__(self, fmt: str | None = "uga") -> None:
+		self._format_data = fmt
+		self.__data_snp = None
+
+	@property
+	def data(self) -> pd.DataFrame | None:
+		return self.__data_snp
+
+	def process(self, data: pd.DataFrame) -> None:
+		""" Data processing and formatting. Calculation of statistical
+		information
+
+		:param data: Data from FinalReport file. Example:
+			SNP Name  Sample ID  Allele1 - AB  Allele2 - AB  GC Score  GT Score
+			ABCA12	14814	A	A	0.4048	0.8164
+			ARS-BFGL-BAC-13031	14814	B	B	0.9083	0.8712
+			ARS-BFGL-BAC-13039	14814	A	A	0.9005	0.9096
+			ARS-BFGL-BAC-13049	14814	A	B	0.9295	0.8926
+
+		:return: Returns true if the data was formatted successfully and
+			statistical information was calculated, false if an error.
+		"""
+
+		if not all(list(map(lambda x: x in data.columns, FIELDS_ILLUMIN))):
+			raise KeyError(
+				'The name of the fields does not match the finalreport.txt '
+				'file from Illumina'
+			)
+
+		self.__data_snp = data.rename(columns=MAP_FIELDS)
+		self.__data_snp['SNP'] = \
+			self.__data_snp[['ALLELE1', 'ALLELE2']].\
+			sum(axis=1).\
+			map(Snp._ALLELE_CODE)
+
+		self.__data_snp = self.__data_snp[Snp._FIELDS].astype(Snp._F_DTYPE)
+
+		if self._format_data is not None and self._format_data == "uga":
+			self.__data_snp = self._format_uga(
+				self.__data_snp[['SAMPLE_ID', 'SNP']]
+			)
+
+	@staticmethod
+	def _format_uga(data: pd.DataFrame) -> pd.DataFrame:
+		""" Data format to use snp in plink and blupf90. """
+
+		return data.groupby(by='SAMPLE_ID').sum().reset_index()
+
+	def to_file(self, file_path: str | Path) -> None:
+		""" Saving data to a file.
+
+		:param file_path: Path to file
+		"""
+
+		if isinstance(file_path, str):
+			file_path = Path(file_path)
+
+		if self._format_data is not None and self._format_data == "uga":
+
+			max_len = self.__data_snp["SAMPLE_ID"].str.len().max()
+
+			self.__data_snp.\
+				apply(
+					lambda x: " ".join([
+						self._add_space(x.iloc[0], max_len), x.iloc[1]
+					]),
+					axis=1
+				).\
+				to_csv(file_path, index=False, header=False)
+
+			self.__data_snp["SAMPLE_ID"] = \
+				self.__data_snp["SAMPLE_ID"].str.strip()
+
+			return None
+
+		self.__data_snp.to_csv(file_path, sep=" ", index=False)
+
+	@staticmethod
+	def _add_space(value: str, max_len: int) -> str:
+		""" Adding spaces up to the maximum length of the value in the
+		sample_id data.
+
+		:param value: Sample_id value
+		:param max_len: Max len sample_id value
+		:return: Return replacing value
+		"""
+		return "".join([value, " " * (max_len - len(value))])

snplib/parentage/__init__.py

@@ -1,15 +1,15 @@
-#!/usr/bin/env python
-# coding: utf-8
-__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
-
-from ._discov import Discovery
-from ._verif import Verification
-from ._isagmark import isag_verif, isag_disc
-
-
-__all__ = [
-	"Discovery",
-	"Verification",
-	"isag_disc",
-	"isag_verif"
-]
+#!/usr/bin/env python
+# coding: utf-8
+__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
+
+from ._discov import Discovery
+from ._verif import Verification
+from ._isagmark import isag_verif, isag_disc
+
+
+__all__ = [
+	"Discovery",
+	"Verification",
+	"isag_disc",
+	"isag_verif"
+]

snplib/parentage/_discov.py

@@ -1,102 +1,102 @@
-#!/usr/bin/env python
-# coding: utf-8
-__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
-
-import pandas as pd
-
-"""
-Search for paternity according to ICAR recommendations
-https://www.icar.org/Documents/GenoEx/ICAR%20Guidelines%20for%20Parentage%20Verification%20and%20Parentage%20Discovery%20based%20on%20SNP.pdf
-"""
-
-
-class Discovery(object):
-    """ Search for paternity according to ICAR recommendations
-
-    :argument isag_markers: Fixed sample of markers to confirm paternity.
-    """
-
-    def __init__(
-            self, isag_markers: pd.Series | list | set | None = None
-    ) -> None:
-        self.__isag_markers = isag_markers
-
-        self.__num_conflicts = None  # Number of conflicts
-        self.__perc_conflicts = None
-
-    @property
-    def status(self) -> None | str:
-        """ The status of each parent discovered. """
-
-        if self.__perc_conflicts is not None:
-            if 0 <= self.__perc_conflicts < 1:
-                return 'Discovered'
-            elif 1 < self.__perc_conflicts < 3:
-                return 'Doubtful'
-            elif self.__perc_conflicts >= 3:
-                return 'Excluded'
-            else:
-                return None
-
-    @property
-    def num_conflicts(self) -> None | int:
-        return self.__num_conflicts
-
-    @property
-    def perc_conflicts(self) -> None | float:
-        return self.__perc_conflicts
-
-    def search_parent(
-            self,
-            data: pd.DataFrame,
-            descendant: str,
-            parents: str,
-            snp_name_col: str
-    ) -> None:
-        """ Search for paternity.
-
-        :param data: SNP data for descendant and parent.
-        :param descendant: Columns name of the descendant in the data.
-        :param parents: Columns name or list name of the parents in the data.
-        :param snp_name_col: SNP columns name is data.
-        """
-
-        if self.__isag_markers is None:
-            raise ValueError("Error. No array of snp names to verify")
-
-        sample_by_markers = data.loc[
-            data[snp_name_col].isin(self.__isag_markers),
-            [snp_name_col, descendant, parents]
-        ]
-
-        # Filtering 5s from a descendent
-        desc_marks = sample_by_markers.loc[
-            sample_by_markers[descendant] != 5, [snp_name_col, descendant]
-        ]
-
-        # According to ICAR, the number of available markers must be
-        # above 450
-        if len(desc_marks) < 450:
-            raise Exception("Calf call rate is low.")
-
-        # Common after filtering markers of potential ancestors
-        sample_parents = sample_by_markers.loc[
-            sample_by_markers[snp_name_col].isin(desc_marks[snp_name_col]),
-            parents
-        ]
-
-        # Number of available markers in potential ancestors
-        prob_parents_same_n_markers = (sample_parents < 5).sum()
-
-        # number of conflicts
-        self.__num_conflicts = (
-            abs(sample_parents.sub(desc_marks[descendant], axis=0)) == 2
-        ).sum()
-
-        # Percentage of conflicts
-        self.__perc_conflicts = (
-            (self.__num_conflicts / prob_parents_same_n_markers) * 100
-        ).round(2)
-
-    def __status_define(self) -> None:
-        ...
+#!/usr/bin/env python
+# coding: utf-8
+__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
+
+import pandas as pd
+
+"""
+Search for paternity according to ICAR recommendations
+https://www.icar.org/Documents/GenoEx/ICAR%20Guidelines%20for%20Parentage%20Verification%20and%20Parentage%20Discovery%20based%20on%20SNP.pdf
+"""
+
+
+class Discovery(object):
+    """ Search for paternity according to ICAR recommendations
+
+    :argument isag_markers: Fixed sample of markers to confirm paternity.
+    """
+
+    def __init__(
+            self, isag_markers: pd.Series | list | set | None = None
+    ) -> None:
+        self.__isag_markers = isag_markers
+
+        self.__num_conflicts = None  # Number of conflicts
+        self.__perc_conflicts = None
+
+    @property
+    def status(self) -> None | str:
+        """ The status of each parent discovered. """
+
+        if self.__perc_conflicts is not None:
+            if 0 <= self.__perc_conflicts < 1:
+                return 'Discovered'
+            elif 1 < self.__perc_conflicts < 3:
+                return 'Doubtful'
+            elif self.__perc_conflicts >= 3:
+                return 'Excluded'
+            else:
+                return None
+
+    @property
+    def num_conflicts(self) -> None | int:
+        return self.__num_conflicts
+
+    @property
+    def perc_conflicts(self) -> None | float:
+        return self.__perc_conflicts
+
+    def search_parent(
+            self,
+            data: pd.DataFrame,
+            descendant: str,
+            parents: str,
+            snp_name_col: str
+    ) -> None:
+        """ Search for paternity.
+
+        :param data: SNP data for descendant and parent.
+        :param descendant: Columns name of the descendant in the data.
+        :param parents: Columns name or list name of the parents in the data.
+        :param snp_name_col: SNP columns name is data.
+        """
+
+        if self.__isag_markers is None:
+            raise ValueError("Error. No array of snp names to verify")
+
+        sample_by_markers = data.loc[
+            data[snp_name_col].isin(self.__isag_markers),
+            [snp_name_col, descendant, parents]
+        ]
+
+        # Filtering 5s from a descendent
+        desc_marks = sample_by_markers.loc[
+            sample_by_markers[descendant] != 5, [snp_name_col, descendant]
+        ]
+
+        # According to ICAR, the number of available markers must be
+        # above 450
+        if len(desc_marks) < 450:
+            raise Exception("Calf call rate is low.")
+
+        # Common after filtering markers of potential ancestors
+        sample_parents = sample_by_markers.loc[
+            sample_by_markers[snp_name_col].isin(desc_marks[snp_name_col]),
+            parents
+        ]
+
+        # Number of available markers in potential ancestors
+        prob_parents_same_n_markers = (sample_parents < 5).sum()
+
+        # number of conflicts
+        self.__num_conflicts = (
+            abs(sample_parents.sub(desc_marks[descendant], axis=0)) == 2
+        ).sum()
+
+        # Percentage of conflicts
+        self.__perc_conflicts = (
+            (self.__num_conflicts / prob_parents_same_n_markers) * 100
+        ).round(2)
+
+    def __status_define(self) -> None:
+        ...

snplib/parentage/_isagmark.py

@@ -1,15 +1,15 @@
-#!/usr/bin/env python
-# coding: utf-8
-__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
-
-from pathlib import Path
-
-import pandas as pd
-
-
-def isag_disc() -> pd.DataFrame:
-	return pd.read_pickle(Path(__file__).parent.joinpath("isag_disc.pl"))
-
-
-def isag_verif() -> pd.DataFrame:
-	return pd.read_pickle(Path(__file__).parent.joinpath("isag_verif.pl"))
+#!/usr/bin/env python
+# coding: utf-8
+__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
+
+from pathlib import Path
+
+import pandas as pd
+
+
+def isag_disc() -> pd.DataFrame:
+	return pd.read_pickle(Path(__file__).parent.joinpath("isag_disc.pl"))
+
+
+def isag_verif() -> pd.DataFrame:
+	return pd.read_pickle(Path(__file__).parent.joinpath("isag_verif.pl"))