snplib 1.0.10__tar.gz → 1.1.10__tar.gz

{snplib-1.0.10 → snplib-1.1.10}/.gitignore

@@ -17,6 +17,8 @@
 !requirements.txt
 !/tests/*/**
 !/docs/*/**
+/docs/_build
+
 
 *.idea*
 *__pycache__*

{snplib-1.0.10/src/snplib.egg-info → snplib-1.1.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: snplib
-Version: 1.0.10
+Version: 1.1.10
 Summary: Snptools is a tool for Single Nucleotide Polymorphism (SNP) data processing
 Author-email: Igor <igor.loschinin@gmail.com>
 License: GNU
@@ -10,14 +10,14 @@ 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: numpy>=2.2.3
+Requires-Dist: pandas>=2.2.3
+Requires-Dist: six>=1.17.0
 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: XlsxWriter>=3.2.2
+Requires-Dist: openpyxl>=3.1.5
+Requires-Dist: pydantic>=2.10.6
 
 # snptools
 <p align="center">

{snplib-1.0.10 → snplib-1.1.10}/docs/conf.py

@@ -8,7 +8,7 @@
 
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../src/snplib'))
+sys.path.insert(0, os.path.abspath('../src'))
 
 project = 'snptools'
 copyright = '2025, Igor Locshinin'

{snplib-1.0.10 → snplib-1.1.10}/docs/examples.rst

@@ -90,7 +90,19 @@ plink - GBLUP, ssGBLUP, GWAS.
 blupf90 format
 ______________
 The input data for obtaining the ``snp.txt`` file used for the genomic
-blupf90 evaluation is the data file - processed file ``finalreport.txt``
+blupf90 evaluation is the data file - processed file ``finalreport.txt``.
+The processed file can be seen in the item above - Finalreport.txt processing:
+
+Content input *file.txt*::
+
+        SNP Name    Sample ID    Allele1 - AB  Allele2 - AB     GC Score    X Y
+        ARS-BFGL-BAC-10172 HO840M003135245650 B B 0.9420 0.069 0.801
+        ARS-BFGL-BAC-1020 HO840M003135245650 B B 0.9489 0.033 0.700
+        ARS-BFGL-BAC-10245 HO840M003135245650 B B 0.7277 0.152 1.504
+        ARS-BFGL-BAC-10345 HO840M003135245650 A B 0.9411 0.598 0.572
+        ARS-BFGL-BAC-10375 HO840M003135245650 A B 0.9348 0.430 0.494f
+
+        ...
 
 **uga**
 
@@ -99,7 +111,7 @@ blupf90 evaluation is the data file - processed file ``finalreport.txt``
     import pandas as pd
     from snplib.format import Snp
 
-    data_finalreport = pd.read_csv("file.txt", sep="\t")
+    data_finalreport = pd.read_csv("path_to_file/file.txt", sep="\t")
 
     obj = Snp(fmt="uga")
     obj_snp.process(data_finalreport)
@@ -111,7 +123,7 @@ Data after snp processing in ``uga`` (blupf90) format - obj_snp.data::
     0     14814  02011015010000500
     1     14815  01110152120222512
 
-Default result::
+Default result - this is what the data looks like if ``fmt=None``::
 
                     SNP_NAME SAMPLE_ID SNP
     0               ABCA12     14814   0
@@ -130,16 +142,104 @@ ____________
 
 This page describes specialized PLINK input and output file formats which are
 identifiable by file extension. https://www.cog-genomics.org/plink/1.9/formats
-Распространненные фомраты для проведения GWAS анализа - ``ped``, ``map``, ``fam``, ``lgen``...
+Common fomrats for performing GWAS analysis - ``ped``, ``map``, ``fam``, ``lgen``....
 
 **map** - https://www.cog-genomics.org/plink/1.9/formats#map
 
+To get the ``.map`` file, first you need to download the *manifest file* for the chip
+you are using chip.
+
+.. note::
+    *file_bovinesnp50.csv* - The file that is taken on the Illumina website with full
+    information about the chip https://support.illumina.com/downloads/bovinesnp50-v3-0-product-files.html
+
+Since the make_map function accepts **pd.DataFrame**, the *manifest file* processing is performed
+independently.
+
+Input data for make_map::
+
+                                           IlmnID  ... BeadSetID
+    0       BovineHD0100037694-128_T_F_2278925834  ...      1241
+    1   BovineHD0100037699_dup-128_T_F_2327674593  ...      1241
+    2   BovineHD0100037703_dup-128_B_R_2327674602  ...      1241
+    3   BovineHD0100037704_dup-128_T_F_2327674603  ...      1241
+    4   BovineHD0100037710_dup-128_T_F_2327674613  ...      1241
+    5   BovineHD0100037712_dup-128_B_R_2327674618  ...      1241
+    6       BovineHD0100037716-128_T_F_2255347065  ...      1241
+    7       BovineHD0100037719-128_T_F_2278926219  ...      1241
+    8       BovineHD0100037720-128_B_R_2255342455  ...      1241
+    9   BovineHD0100037722_dup-128_B_R_2327674634  ...      1241
+
+
+.. note::
+    The original file, for example, **BovineSNP50_v3_A1.csv** looks like this::
+
+        Illumina, Inc.,,,,,,,,,,,,,,,,,
+        [Heading],,,,,,,,,,,,,,,,,,
+        Descriptor File Name,BovineSNP50_v3_A1.bpm,,,,,,,,,,,,,,,,,
+        Assay Format,Infinium HTS,,,,,,,,,,,,,,,,,
+        Date Manufactured,1/14/2016,,,,,,,,,,,,,,,,,
+        Loci Count ,53218,,,,,,,,,,,,,,,,,
+        [Assay],,,,,,,,,,,,,,,,,,
+        IlmnID,Name,IlmnStrand,SNP,AddressA_ID,AlleleA_ProbeSeq,AddressB_ID,AlleleB_ProbeSeq,GenomeBuild,Chr,MapInfo,Ploidy,Species,Source,SourceVersion,SourceStrand,SourceSeq,TopGenomicSeq,BeadSetID
+        ABCA12_r2-1_T_F_2277749139,ABCA12,TOP,[A/G],0059616496,CTTGTCTTCTTTTGGAATGTTACAGGTATGGTATGATCCAGAAGGCTATC,,,0,2,103548215,diploid,Bos taurus,UMD3.1,1,TOP,ACTCTGGTGGATGGTTCATAATCTGCTAAGATGAATAAGTTACTGGGGAAACTGGTGCATTTATTTTAAATATAAATTATATAGTCTGTAAGATATAAAGACTGCCTAATTTATTTGAACACCATACTGATCTTGTCTTCTTTTGGAATGTTACAGGTATGGTATGATCCAGAAGGCTATC[A/G]CTCCCTTCCAGCTTACCTCAACAGCCTGAATAATTTCCTCCTGCGAGTTAACATGTCAAAATATGATGCTGCCCGACATGGTAAAGTTATTTACATAGGAGCTCCTTGTATTGAAACTCTTGCTACTCTCCATGTGAAAATATACATTAGACCCCATTTTCCTCCCTGTGGCAGCTAT,ACTCTGGTGGATGGTTCATAATCTGCTAAGATGAATAAGTTACTGGGGAAACTGGTGCATTTATTTTAAATATAAATTATATAGTCTGTAAGATATAAAGACTGCCTAATTTATTTGAACACCATACTGATCTTGTCTTCTTTTGGAATGTTACAGGTATGGTATGATCCAGAAGGCTATC[A/G]CTCCCTTCCAGCTTACCTCAACAGCCTGAATAATTTCCTCCTGCGAGTTAACATGTCAAAATATGATGCTGCCCGACATGGTAAAGTTATTTACATAGGAGCTCCTTGTATTGAAACTCTTGCTACTCTCCATGTGAAAATATACATTAGACCCCATTTTCCTCCCTGTGGCAGCTAT,1241
+        APAF1_dup-1_B_F_2327661418,APAF1,BOT,[T/C],0041654401,ATATTGTGCAACTGGGCCTCTGTGAACTGGAAACTTCAGAGGTTTATCGG,,,0,5,63150400,diploid,Bos taurus,UMD3.1,1,BOT,CCATTTCCTAATATTGTGCAACTGGGCCTCTGTGAACTGGAAACTTCAGAGGTTTATCGG[T/C]AAGCTAAGCTGCAGGCCAAGCAGGAGGTCGATAACGGAATGCTTTACCTGGAGTGGGTGT,ACACCCACTCCAGGTAAAGCATTCCGTTATCGACCTCCTGCTTGGCCTGCAGCTTAGCTT[A/G]CCGATAAACCTCTGAAGTTTCCAGTTCACAGAGGCCCAGTTGCACAATATTAGGAAATGG,1241
+        ARS-BFGL-BAC-10172_dup-0_T_F_2328966397,ARS-BFGL-BAC-10172,TOP,[A/G],0072620471,GGTCCCCAAAGTATGTGGTAGCACTTACTTATGTAAGTCATCACTCAAGT,,,3,14,6371334,diploid,Bos taurus,UM3,0,TOP,CTCAGAAGTTGGTCCCCAAAGTATGTGGTAGCACTTACTTATGTAAGTCATCACTCAAGT[A/G]ATCCAGAATATTCTTTTAGTAATATTTTTGTTAATATTGAAATTTTTAAAACAATTGAAA,CTCAGAAGTTGGTCCCCAAAGTATGTGGTAGCACTTACTTATGTAAGTCATCACTCAAGT[A/G]ATCCAGAATATTCTTTTAGTAATATTTTTGTTAATATTGAAATTTTTAAAACAATTGAAA,1241
+        .
+        .
+        .
+        UA-IFASA-9812_dup-0_B_F_2329051536,UA-IFASA-9812,BOT,[T/C],0031677304,ACCTCCATAGCTGATAGGAATGGTCTCAACTTGCAGCCCCATTATACTAA,,,3,29,48012818,diploid,Bos taurus,UM3,0,BOT,GTAAAAACAAACCTCCATAGCTGATAGGAATGGTCTCAACTTGCAGCCCCATTATACTAA[T/C]GATGATCTGAAGTTTCTCAAGCACGCAGAGAAACGTAAGAGAAACGTTCCAGCAAAGGGA,TCCCTTTGCTGGAACGTTTCTCTTACGTTTCTCTGCGTGCTTGAGAAACTTCAGATCATC[A/G]TTAGTATAATGGGGCTGCAAGTTGAGACCATTCCTATCAGCTATGGAGGTTTGTTTTTAC,1241
+        UA-IFASA-9813_dup-0_B_F_2329051538,UA-IFASA-9813,BOT,[T/C],0011661313,ACCTTTGCACTCGCTAACGGTTCAGCATTAATCAGACTTCCTCAGGAATT,,,3,19,32508700,diploid,Bos taurus,UM3,0,BOT,AATAAAACCAACCTTTGCACTCGCTAACGGTTCAGCATTAATCAGACTTCCTCAGGAATT[T/C]AGGGGTCAATTCCCCCATGTCTAAAATTGAACCTCAACGTCCTTTCTGTTTTCAAAACTC,GAGTTTTGAAAACAGAAAGGACGTTGAGGTTCAATTTTAGACATGGGGGAATTGACCCCT[A/G]AATTCCTGAGGAAGTCTGATTAATGCTGAACCGTTAGCGAGTGCAAAGGTTGGTTTTATT,1241
+        UMPS_dup-1_T_R_2327737250,UMPS,TOP,[A/G],0073777348,TAACTGAACTCCTGGAGTCAAGTGAAGAAATTCTGGTTTCATGCTTACTC,,,0,1,69756880,diploid,Bos taurus,UMD3.1,1,BOT,TCATCTGTTGATTACATTCCATTCAGGTGCAAATGGCTGAAGAACATTCTGAATTTGTGATTGGTTTTATTTCTGGCTCC[T/C]GAGTAAGCATGAAACCAGAATTTCTTCACTTGACTCCAGGAGTTCAGTTAGAAGCAGGAGGTAAGCCTATTGATTGGTAA,TTACCAATCAATAGGCTTACCTCCTGCTTCTAACTGAACTCCTGGAGTCAAGTGAAGAAATTCTGGTTTCATGCTTACTC[A/G]GGAGCCAGAAATAAAACCAATCACAAATTCAGAATGTTCTTCAGCCATTTGCACCTGAATGGAATGTAATCAACAGATGA,1241
+        [Controls],,,,,,,,,,,,,,,,,,
+        0027630314,Staining,Red,DNP (High),,,,,,,,,,,,,,,
+        0029619375,Staining,Purple,DNP (Bgnd),,,,,,,,,,,,,,,
+        0041666334,Staining,Green,Biotin (High),,,,,,,,,,,,,,,
+        0034648333,Staining,Blue,Biotin (Bgnd),,,,,,,,,,,,,,,
+        0017616306,Extension,Red,Extension (A),,,,,,,,,,,,,,,
+        0014607337,Extension,Purple,Extension (T),,,,,,,,,,,,,,,
+
+    Therefore, for direct reading via **pd.read_csv()** it is necessary to
+    preprocess the file - delete extra lines::
+
+        Illumina, Inc.,,,,,,,,,,,,,,,,,
+        [Heading],,,,,,,,,,,,,,,,,,
+        Descriptor File Name,BovineSNP50_v3_A1.bpm,,,,,,,,,,,,,,,,,
+        Assay Format,Infinium HTS,,,,,,,,,,,,,,,,,
+        Date Manufactured,1/14/2016,,,,,,,,,,,,,,,,,
+        Loci Count ,53218,,,,,,,,,,,,,,,,,
+        [Assay],,,,,,,,,,,,,,,,,,
+
+        and
+
+        [Controls],,,,,,,,,,,,,,,,,,
+        0027630314,Staining,Red,DNP (High),,,,,,,,,,,,,,,
+        0029619375,Staining,Purple,DNP (Bgnd),,,,,,,,,,,,,,,
+        0041666334,Staining,Green,Biotin (High),,,,,,,,,,,,,,,
+        0034648333,Staining,Blue,Biotin (Bgnd),,,,,,,,,,,,,,,
+        0017616306,Extension,Red,Extension (A),,,,,,,,,,,,,,,
+        0014607337,Extension,Purple,Extension (T),,,,,,,,,,,,,,,
+
+    The file should end up looking like this::
+
+        IlmnID,Name,IlmnStrand,SNP,AddressA_ID,AlleleA_ProbeSeq,AddressB_ID,AlleleB_ProbeSeq,GenomeBuild,Chr,MapInfo,Ploidy,Species,Source,SourceVersion,SourceStrand,SourceSeq,TopGenomicSeq,BeadSetID
+        ABCA12_r2-1_T_F_2277749139,ABCA12,TOP,[A/G],0059616496,CTTGTCTTCTTTTGGAATGTTACAGGTATGGTATGATCCAGAAGGCTATC,,,0,2,103548215,diploid,Bos taurus,UMD3.1,1,TOP,ACTCTGGTGGATGGTTCATAATCTGCTAAGATGAATAAGTTACTGGGGAAACTGGTGCATTTATTTTAAATATAAATTATATAGTCTGTAAGATATAAAGACTGCCTAATTTATTTGAACACCATACTGATCTTGTCTTCTTTTGGAATGTTACAGGTATGGTATGATCCAGAAGGCTATC[A/G]CTCCCTTCCAGCTTACCTCAACAGCCTGAATAATTTCCTCCTGCGAGTTAACATGTCAAAATATGATGCTGCCCGACATGGTAAAGTTATTTACATAGGAGCTCCTTGTATTGAAACTCTTGCTACTCTCCATGTGAAAATATACATTAGACCCCATTTTCCTCCCTGTGGCAGCTAT,ACTCTGGTGGATGGTTCATAATCTGCTAAGATGAATAAGTTACTGGGGAAACTGGTGCATTTATTTTAAATATAAATTATATAGTCTGTAAGATATAAAGACTGCCTAATTTATTTGAACACCATACTGATCTTGTCTTCTTTTGGAATGTTACAGGTATGGTATGATCCAGAAGGCTATC[A/G]CTCCCTTCCAGCTTACCTCAACAGCCTGAATAATTTCCTCCTGCGAGTTAACATGTCAAAATATGATGCTGCCCGACATGGTAAAGTTATTTACATAGGAGCTCCTTGTATTGAAACTCTTGCTACTCTCCATGTGAAAATATACATTAGACCCCATTTTCCTCCCTGTGGCAGCTAT,1241
+        APAF1_dup-1_B_F_2327661418,APAF1,BOT,[T/C],0041654401,ATATTGTGCAACTGGGCCTCTGTGAACTGGAAACTTCAGAGGTTTATCGG,,,0,5,63150400,diploid,Bos taurus,UMD3.1,1,BOT,CCATTTCCTAATATTGTGCAACTGGGCCTCTGTGAACTGGAAACTTCAGAGGTTTATCGG[T/C]AAGCTAAGCTGCAGGCCAAGCAGGAGGTCGATAACGGAATGCTTTACCTGGAGTGGGTGT,ACACCCACTCCAGGTAAAGCATTCCGTTATCGACCTCCTGCTTGGCCTGCAGCTTAGCTT[A/G]CCGATAAACCTCTGAAGTTTCCAGTTCACAGAGGCCCAGTTGCACAATATTAGGAAATGG,1241
+        ARS-BFGL-BAC-10172_dup-0_T_F_2328966397,ARS-BFGL-BAC-10172,TOP,[A/G],0072620471,GGTCCCCAAAGTATGTGGTAGCACTTACTTATGTAAGTCATCACTCAAGT,,,3,14,6371334,diploid,Bos taurus,UM3,0,TOP,CTCAGAAGTTGGTCCCCAAAGTATGTGGTAGCACTTACTTATGTAAGTCATCACTCAAGT[A/G]ATCCAGAATATTCTTTTAGTAATATTTTTGTTAATATTGAAATTTTTAAAACAATTGAAA,CTCAGAAGTTGGTCCCCAAAGTATGTGGTAGCACTTACTTATGTAAGTCATCACTCAAGT[A/G]ATCCAGAATATTCTTTTAGTAATATTTTTGTTAATATTGAAATTTTTAAAACAATTGAAA,1241
+        .
+        .
+        .
+        UA-IFASA-9812_dup-0_B_F_2329051536,UA-IFASA-9812,BOT,[T/C],0031677304,ACCTCCATAGCTGATAGGAATGGTCTCAACTTGCAGCCCCATTATACTAA,,,3,29,48012818,diploid,Bos taurus,UM3,0,BOT,GTAAAAACAAACCTCCATAGCTGATAGGAATGGTCTCAACTTGCAGCCCCATTATACTAA[T/C]GATGATCTGAAGTTTCTCAAGCACGCAGAGAAACGTAAGAGAAACGTTCCAGCAAAGGGA,TCCCTTTGCTGGAACGTTTCTCTTACGTTTCTCTGCGTGCTTGAGAAACTTCAGATCATC[A/G]TTAGTATAATGGGGCTGCAAGTTGAGACCATTCCTATCAGCTATGGAGGTTTGTTTTTAC,1241
+        UA-IFASA-9813_dup-0_B_F_2329051538,UA-IFASA-9813,BOT,[T/C],0011661313,ACCTTTGCACTCGCTAACGGTTCAGCATTAATCAGACTTCCTCAGGAATT,,,3,19,32508700,diploid,Bos taurus,UM3,0,BOT,AATAAAACCAACCTTTGCACTCGCTAACGGTTCAGCATTAATCAGACTTCCTCAGGAATT[T/C]AGGGGTCAATTCCCCCATGTCTAAAATTGAACCTCAACGTCCTTTCTGTTTTCAAAACTC,GAGTTTTGAAAACAGAAAGGACGTTGAGGTTCAATTTTAGACATGGGGGAATTGACCCCT[A/G]AATTCCTGAGGAAGTCTGATTAATGCTGAACCGTTAGCGAGTGCAAAGGTTGGTTTTATT,1241
+        UMPS_dup-1_T_R_2327737250,UMPS,TOP,[A/G],0073777348,TAACTGAACTCCTGGAGTCAAGTGAAGAAATTCTGGTTTCATGCTTACTC,,,0,1,69756880,diploid,Bos taurus,UMD3.1,1,BOT,TCATCTGTTGATTACATTCCATTCAGGTGCAAATGGCTGAAGAACATTCTGAATTTGTGATTGGTTTTATTTCTGGCTCC[T/C]GAGTAAGCATGAAACCAGAATTTCTTCACTTGACTCCAGGAGTTCAGTTAGAAGCAGGAGGTAAGCCTATTGATTGGTAA,TTACCAATCAATAGGCTTACCTCCTGCTTCTAACTGAACTCCTGGAGTCAAGTGAAGAAATTCTGGTTTCATGCTTACTC[A/G]GGAGCCAGAAATAAAACCAATCACAAATTCAGAATGTTCTTCAGCCATTTGCACCTGAATGGAATGTAATCAACAGATGA,1241
+
+
 .. code-block:: python
 
     import pandas as pd
     from snplib.format import make_map
 
-    input_data = pd.read_csv(DIR_FILES / "./file_bovinesnp50.csv")
+    input_data = pd.read_csv("./file_bovinesnp50.csv")
     data_map = make_map(input_data)
 
 Output data view::
@@ -150,12 +250,6 @@ Output data view::
          0  BovineHD0100037703        0        0
          0  BovineHD0100037704        0        0
 
-.. note::
-    file_bovinesnp50.csv - The file that is taken on the Illumina website with full
-    information about the chip
-    https://support.illumina.com/downloads/bovinesnp50-v3-0-product-files.html
-
-
 **ped** - https://www.cog-genomics.org/plink/1.9/formats#ped
 
 .. code-block:: python

snplib-1.1.10/docs/requirements.txt

@@ -0,0 +1,2 @@
+sphinx==8.1.3
+sphinx_rtd_theme==3.0.2

{snplib-1.0.10 → snplib-1.1.10}/pyproject.toml

@@ -17,7 +17,7 @@ snplib = ["*.pl"]
 
 [project]
 name = "snplib"
-version = "1.0.10"
+version = "1.1.10"
 description = "Snptools is a tool for Single Nucleotide Polymorphism (SNP) data processing"
 authors = [
     {name = "Igor", email = "igor.loschinin@gmail.com"}
@@ -30,14 +30,14 @@ classifiers = [
     "Operating System :: OS Independent",
 ]
 dependencies = [
-    "numpy>=1.26.1",
-    "pandas>=2.1.1",
-    "six>=1.16.0",
+    "numpy>=2.2.3",
+    "pandas>=2.2.3",
+    "six>=1.17.0",
     "swifter>=1.4.0",
     "xlrd>=2.0.1",
-    "XlsxWriter>=3.1.9",
-    "openpyxl>=3.1.2",
-    "pydantic>=2.4.2",
+    "XlsxWriter>=3.2.2",
+    "openpyxl>=3.1.5",
+    "pydantic>=2.10.6",
 ]
 
 [project.urls]

snplib-1.1.10/requirements.txt

@@ -0,0 +1,10 @@
+numpy==2.2.3
+pandas==2.2.3
+six==1.17.0
+swifter==1.4.0
+xlrd==2.0.1
+XlsxWriter==3.2.2
+openpyxl==3.1.5
+pydantic==2.10.6
+pytest==8.3.4
+setuptools-scm==8.1.0

{snplib-1.0.10 → snplib-1.1.10}/src/snplib/finalreport/_finalreport.py

@@ -7,11 +7,15 @@ 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 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
@@ -235,17 +239,15 @@ class FinalReport(object):
 		if self._check_on_ru_symbols(self._map_rn.UNIQ_KEY):
 			raise Exception("Error. Unique keys contain Cyrillic alphabet.")
 
-		if self._map_rn.UNIQ_KEY.isna().any():
-			self._map_rn.fillna('unknown', inplace=True)
-
 	@staticmethod
 	def _check_on_ru_symbols(seq: pd.Series) -> bool | None:
-		"""
+		""" Checial verification of the Cyrillic
 
-		:param seq:
-		:return:
+		:param seq: Squeezed for verification.
+		:return: Truth if there are no symbols of Cyril and there is a lie if
+			there is.
 		"""
 
-		return any(seq.apply(lambda x: bool(re.search('[а-яА-Я]', x))))
-
-
+		return seq.apply(
+			lambda x: bool(re.search('[а-яА-Я]', x)) if x is not nan else x
+		).any()

{snplib-1.0.10 → snplib-1.1.10/src/snplib.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: snplib
-Version: 1.0.10
+Version: 1.1.10
 Summary: Snptools is a tool for Single Nucleotide Polymorphism (SNP) data processing
 Author-email: Igor <igor.loschinin@gmail.com>
 License: GNU
@@ -10,14 +10,14 @@ 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: numpy>=2.2.3
+Requires-Dist: pandas>=2.2.3
+Requires-Dist: six>=1.17.0
 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: XlsxWriter>=3.2.2
+Requires-Dist: openpyxl>=3.1.5
+Requires-Dist: pydantic>=2.10.6
 
 # snptools
 <p align="center">

{snplib-1.0.10 → snplib-1.1.10}/src/snplib.egg-info/SOURCES.txt

@@ -63,6 +63,10 @@ tests/finalreport/files/fr/file6.txt
 tests/finalreport/files/fr/file6.xlsx
 tests/finalreport/files/fr/file7.txt
 tests/finalreport/files/fr/file7.xlsx
+tests/finalreport/files/fr/file8.txt
+tests/finalreport/files/fr/file8.xlsx
+tests/finalreport/files/fr/file9.txt
+tests/finalreport/files/fr/file9.xlsx
 tests/format/__init__.py
 tests/format/test_plink_fam.py
 tests/format/test_plink_lgen.py

snplib-1.1.10/src/snplib.egg-info/requires.txt

@@ -0,0 +1,8 @@
+numpy>=2.2.3
+pandas>=2.2.3
+six>=1.17.0
+swifter>=1.4.0
+xlrd>=2.0.1
+XlsxWriter>=3.2.2
+openpyxl>=3.1.5
+pydantic>=2.10.6

snplib-1.1.10/tests/finalreport/files/fr/file8.txt

@@ -0,0 +1,28 @@
+[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
+ARS-BFGL-BAC-10172	1	B	B	0.9140	0.8767
+ARS-BFGL-BAC-1020	1	B	B	0.9288	0.8919
+ARS-BFGL-BAC-10245	1	B	B	0.7227	0.7447
+ARS-BFGL-BAC-10345	1	A	B	0.9468	0.9127
+ABCA12	2	A	A	0.4048	0.8164
+APAF1	2	B	B	0.9067	0.9155
+ARS-BFGL-BAC-10172	2	A	B	0.9140	0.8767
+ARS-BFGL-BAC-1020	2	A	B	0.9288	0.8919
+ARS-BFGL-BAC-10245	2	A	A	0.7227	0.7447
+ARS-BFGL-BAC-10345	2	B	B	0.9468	0.9127
+ABCA12	3	A	A	0.4048	0.8164
+APAF1	3	B	B	0.9067	0.9155
+ARS-BFGL-BAC-10172	3	A	B	0.9140	0.8767
+ARS-BFGL-BAC-1020	3	A	B	0.9288	0.8919
+ARS-BFGL-BAC-10245	3	A	A	0.7227	0.7447
+ARS-BFGL-BAC-10345	3	A	B	0.9468	0.9127

snplib-1.1.10/tests/finalreport/files/fr/file9.txt

@@ -0,0 +1,28 @@
+[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
+ARS-BFGL-BAC-10172	1	B	B	0.9140	0.8767
+ARS-BFGL-BAC-1020	1	B	B	0.9288	0.8919
+ARS-BFGL-BAC-10245	1	B	B	0.7227	0.7447
+ARS-BFGL-BAC-10345	1	A	B	0.9468	0.9127
+ABCA12	2	A	A	0.4048	0.8164
+APAF1	2	B	B	0.9067	0.9155
+ARS-BFGL-BAC-10172	2	A	B	0.9140	0.8767
+ARS-BFGL-BAC-1020	2	A	B	0.9288	0.8919
+ARS-BFGL-BAC-10245	2	A	A	0.7227	0.7447
+ARS-BFGL-BAC-10345	2	B	B	0.9468	0.9127
+ABCA12	3	A	A	0.4048	0.8164
+APAF1	3	B	B	0.9067	0.9155
+ARS-BFGL-BAC-10172	3	A	B	0.9140	0.8767
+ARS-BFGL-BAC-1020	3	A	B	0.9288	0.8919
+ARS-BFGL-BAC-10245	3	A	A	0.7227	0.7447
+ARS-BFGL-BAC-10345	3	A	B	0.9468	0.9127

{snplib-1.0.10 → snplib-1.1.10}/tests/finalreport/test_finalreport.py

@@ -192,6 +192,7 @@ class TestFinalReport(object):
 
 	@pytest.mark.parametrize("report", ["AB"], indirect=True)
 	def test_7(self, report: FinalReport) -> None:
+		""" An error is checked if the name of the number is Kirilitsa """
 
 		with pytest.raises(
 			Exception, match="Error. Unique keys contain Cyrillic alphabet."
@@ -200,16 +201,29 @@ class TestFinalReport(object):
 				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:
-	# 	...
+		assert report.snp_data is None
+
+	@pytest.mark.parametrize("report", ["AB"], indirect=True)
+	def test_8(self, report: FinalReport) -> None:
+		""" Checking for processing empty values in SID """
+
+		report.handle(
+			DIR_FILES / "fr/file8.txt",
+			DIR_FILES / "fr/file8.xlsx"
+		)
+
+		assert report.snp_data is not None
+		assert not report.snp_data.empty
+		assert report.snp_data['Sample ID'].isna().any()
+
+	@pytest.mark.parametrize("report", ["AB"], indirect=True)
+	def test_9(self, report: FinalReport) -> None:
+		""" Checking for missing values in SID """
+		report.handle(
+			DIR_FILES / "fr/file9.txt",
+			DIR_FILES / "fr/file9.xlsx"
+		)
+
+		assert report.snp_data is not None
+		assert not report.snp_data.empty
+		assert report.snp_data['Sample ID'].isna().any()

snplib-1.0.10/docs/requirements.txt

@@ -1,2 +0,0 @@
-sphinx==7.2.6
-sphinx_rtd_theme==1.3.0

snplib-1.0.10/requirements.txt

@@ -1,12 +0,0 @@
-numpy==1.26.1
-pandas==2.1.1
-six==1.16.0
-swifter==1.4.0
-xlrd==2.0.1
-XlsxWriter==3.1.9
-openpyxl==3.1.2
-pydantic==2.4.2
-pytest==7.4.2
-twine==6.0.1
-build==1.2.2.post1
-setuptools-scm==8.1.0

snplib-1.0.10/src/snplib.egg-info/requires.txt

@@ -1,8 +0,0 @@
-numpy>=1.26.1
-pandas>=2.1.1
-six>=1.16.0
-swifter>=1.4.0
-xlrd>=2.0.1
-XlsxWriter>=3.1.9
-openpyxl>=3.1.2
-pydantic>=2.4.2