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

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (21) hide show
  1. snplib/__init__.py +8 -8
  2. snplib/finalreport/__init__.py +7 -7
  3. snplib/finalreport/_finalreport.py +305 -253
  4. snplib/format/__init__.py +19 -19
  5. snplib/format/__settings.py +7 -7
  6. snplib/format/_plink.py +291 -291
  7. snplib/format/_snp.py +113 -113
  8. snplib/parentage/__init__.py +15 -15
  9. snplib/parentage/_discov.py +102 -102
  10. snplib/parentage/_isagmark.py +15 -15
  11. snplib/parentage/_verif.py +91 -91
  12. snplib/statistics/__init__.py +16 -16
  13. snplib/statistics/_callrate.py +60 -60
  14. snplib/statistics/_freq.py +67 -67
  15. snplib/statistics/_snphwe.py +132 -132
  16. {snplib-1.1.10.dist-info → snplib-1.2.11.dist-info}/LICENSE +674 -674
  17. {snplib-1.1.10.dist-info → snplib-1.2.11.dist-info}/METADATA +80 -80
  18. snplib-1.2.11.dist-info/RECORD +22 -0
  19. {snplib-1.1.10.dist-info → snplib-1.2.11.dist-info}/WHEEL +1 -1
  20. snplib-1.1.10.dist-info/RECORD +0 -22
  21. {snplib-1.1.10.dist-info → snplib-1.2.11.dist-info}/top_level.txt +0 -0
{snplib-1.1.10.dist-info → snplib-1.2.11.dist-info}/METADATA RENAMED
@@ -1,80 +1,80 @@
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- Metadata-Version: 2.2
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- Name: snplib
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- Version: 1.1.10
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- Summary: Snptools is a tool for Single Nucleotide Polymorphism (SNP) data processing
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- Author-email: Igor <igor.loschinin@gmail.com>
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- License: GNU
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- Project-URL: Homepage, https://github.com/IgorekLoschinin/snptools
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- Classifier: Programming Language :: Python :: 3
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- Classifier: Operating System :: OS Independent
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- Requires-Python: >=3.10
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- Description-Content-Type: text/markdown
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- License-File: LICENSE
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- Requires-Dist: numpy>=2.2.3
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- Requires-Dist: pandas>=2.2.3
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- Requires-Dist: six>=1.17.0
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- Requires-Dist: swifter>=1.4.0
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- Requires-Dist: xlrd>=2.0.1
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- Requires-Dist: XlsxWriter>=3.2.2
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- Requires-Dist: openpyxl>=3.1.5
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- Requires-Dist: pydantic>=2.10.6
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-
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- # snptools
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- <p align="center">
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- <img width="150" height="150" src="./iconlib.png">
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- </p>
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-
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- **Snptools** is a tool for SNP (Single Nucleotide Polymorphism) data processing,
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- parentage calculation and call rate estimation.
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-
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- ## Introduction
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-
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- SNP (Single Nucleotide Polymorphism) represent genetic variations, that can
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- be used to analyze genetic data. SNPTools provides a set of tools for working
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- with SNP data, including the following capabilities:
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-
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- - SNP data processing - FinalReport.
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- - Parentage Verification and Parentage Discovery Based on SNP Genotypes (ICAR).
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- - Call rate estimation (percentage of missing data).
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- - Processing and preparation of data in plink formats.
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-
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- ## Installation
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- You can install snptools via pip from [PyPI](https://pypi.org/project/snplib/):
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- ```
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- pip install snplib
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- ```
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-
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- ## Usage
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- Snptools provides commands for a variety of operations. Here are examples of
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- usage:
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-
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- #### SNP data processing:
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- ```
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- from snplib import FinalReport
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- ```
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-
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- #### Computation of parentage:
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- ```
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- from snplib import Discovery, Verification
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- ```
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-
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- #### Preparation format files:
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- ```
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- from snplib import (
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- Snp, make_fam, make_ped, make_lgen, make_map
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- )
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- ```
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-
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- #### Stat:
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- ```
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- from snplib import (
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- hwe, hwe_test, call_rate, allele_freq, minor_allele_freq
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- )
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- ```
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-
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- ## Documentation
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- Detailed documentation on how to use SNPTools is available see the [docs](https://snptools.readthedocs.io/en/latest/).
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-
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- ## License
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- This project is licensed under the GNU General Public License - see the
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- LICENSE file for details.
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+ Metadata-Version: 2.2
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+ Name: snplib
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+ Version: 1.2.11
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+ Summary: Snptools is a tool for Single Nucleotide Polymorphism (SNP) data processing
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+ Author-email: Igor <igor.loschinin@gmail.com>
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+ License: GNU
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+ Project-URL: Homepage, https://github.com/IgorekLoschinin/snptools
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+ Classifier: Programming Language :: Python :: 3
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+ Classifier: Operating System :: OS Independent
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+ Requires-Python: >=3.10
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+ Description-Content-Type: text/markdown
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+ License-File: LICENSE
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+ Requires-Dist: numpy>=2.2.3
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+ Requires-Dist: pandas>=2.2.3
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+ Requires-Dist: six>=1.17.0
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+ Requires-Dist: swifter>=1.4.0
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+ Requires-Dist: xlrd>=2.0.1
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+ Requires-Dist: XlsxWriter>=3.2.2
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+ Requires-Dist: openpyxl>=3.1.5
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+ Requires-Dist: pydantic>=2.10.6
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+
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+ # snptools
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+ <p align="center">
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+ <img width="150" height="150" src="./iconlib.png">
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+ </p>
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+
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+ **Snptools** is a tool for SNP (Single Nucleotide Polymorphism) data processing,
28
+ parentage calculation and call rate estimation.
29
+
30
+ ## Introduction
31
+
32
+ SNP (Single Nucleotide Polymorphism) represent genetic variations, that can
33
+ be used to analyze genetic data. SNPTools provides a set of tools for working
34
+ with SNP data, including the following capabilities:
35
+
36
+ - SNP data processing - FinalReport.
37
+ - Parentage Verification and Parentage Discovery Based on SNP Genotypes (ICAR).
38
+ - Call rate estimation (percentage of missing data).
39
+ - Processing and preparation of data in plink formats.
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+
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+ ## Installation
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+ You can install snptools via pip from [PyPI](https://pypi.org/project/snplib/):
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+ ```
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+ pip install snplib
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+ ```
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+
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+ ## Usage
48
+ Snptools provides commands for a variety of operations. Here are examples of
49
+ usage:
50
+
51
+ #### SNP data processing:
52
+ ```
53
+ from snplib import FinalReport
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+ ```
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+
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+ #### Computation of parentage:
57
+ ```
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+ from snplib import Discovery, Verification
59
+ ```
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+
61
+ #### Preparation format files:
62
+ ```
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+ from snplib import (
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+ Snp, make_fam, make_ped, make_lgen, make_map
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+ )
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+ ```
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+
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+ #### Stat:
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+ ```
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+ from snplib import (
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+ hwe, hwe_test, call_rate, allele_freq, minor_allele_freq
72
+ )
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+ ```
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+
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+ ## Documentation
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+ Detailed documentation on how to use SNPTools is available see the [docs](https://snptools.readthedocs.io/en/latest/).
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+
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+ ## License
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+ This project is licensed under the GNU General Public License - see the
80
+ LICENSE file for details.
snplib-1.2.11.dist-info/RECORD ADDED
@@ -0,0 +1,22 @@
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+ snplib/__init__.py,sha256=xw0VDA6vCABCOwfQHF2L2paFnc4Q_ss7OvFLJYjeU-U,204
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+ snplib/finalreport/__init__.py,sha256=yF48v321n31WqnzzX3F_vZ41t0NkeWruJVIOnM1yLj0,168
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+ snplib/finalreport/_finalreport.py,sha256=M22ZkKhV_XsLH1BLTWIE7dFPCQLWANG7e42ckTi4Ars,7822
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+ snplib/format/__init__.py,sha256=nA7SIUSKZumP62yWvstew8ASLsC4Uz__Ywr8roGdc18,280
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+ snplib/format/__settings.py,sha256=UUK1kc3Fnzl9S3U7MQEbGrumyzogKNW0nllys41ymfk,296
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+ snplib/format/_plink.py,sha256=2MfAtCpYoAIcJ-oVcHOs9o27ruoS6qz1MW7H4Co07Wo,10663
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+ snplib/format/_snp.py,sha256=vKUhsNHjfRCXPxNV0wP1xcPM831SOGIu4RPmuLYh-g4,3285
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+ snplib/parentage/__init__.py,sha256=9wgWZxDJA0FfXs8MT-VVF3O7LfZhDh9y-jEV4_wE4-c,295
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+ snplib/parentage/_discov.py,sha256=YHM83V92uIc8wBtKySU3cschikCCg1vc4wY2fWkg5Xc,3282
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+ snplib/parentage/_isagmark.py,sha256=djEKEHn15vEzcovIh2t_r9PLJOztEM40enWZJf1Un44,371
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+ snplib/parentage/_verif.py,sha256=lcfFMZrNC6ymIMU2cel9Dudgqc3OZ6CIASjDUhnos7E,3110
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+ snplib/parentage/isag_disc.pl,sha256=XzjcsnO_kwPg4WaE2YMuZXBNHQ9ixi6pg5n2mfGOuJU,14219
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+ snplib/statistics/__init__.py,sha256=2xN_dUTProTBUzPW3oKi_CZ0QlqjIUlxbtGfsBqLD2c,318
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+ snplib/statistics/_callrate.py,sha256=Lq8cSPRh-xtGFsANKd0YOt1ucWSZjcsk8z_qocpfq6Y,1926
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+ snplib/statistics/_freq.py,sha256=ZxuZLm8vFS60YKMcrTZDNuj1Y22FkqfaFp76R4hivLY,1690
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+ snplib/statistics/_snphwe.py,sha256=lvIuRYYs625tduNa_DU5OfqWUB7fHnXnh5VoSkNQe_Q,3485
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+ snplib-1.2.11.dist-info/LICENSE,sha256=IwGE9guuL-ryRPEKi6wFPI_zOhg7zDZbTYuHbSt_SAk,35823
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+ snplib-1.2.11.dist-info/METADATA,sha256=HLRbRaM-j1SckrH61L4N2pstK1_iqzKaa-FjcAb_0Pc,2264
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+ snplib-1.2.11.dist-info/WHEEL,sha256=jB7zZ3N9hIM9adW7qlTAyycLYW9npaWKLRzaoVcLKcM,91
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+ snplib-1.2.11.dist-info/top_level.txt,sha256=CGCrLXuCSyXPCTwMFQjPxQR7b93FFFft56sAPPun_2g,7
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+ snplib-1.2.11.dist-info/RECORD,,
{snplib-1.1.10.dist-info → snplib-1.2.11.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
1
1
  Wheel-Version: 1.0
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- Generator: setuptools (75.8.1)
2
+ Generator: setuptools (75.8.2)
3
3
  Root-Is-Purelib: true
4
4
  Tag: py3-none-any
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5
 
snplib-1.1.10.dist-info/RECORD DELETED
@@ -1,22 +0,0 @@
1
- snplib/__init__.py,sha256=xhjj4ZywdwCq91GBh1zfBP_TwFW26-KpHcCUUVvMdgI,196
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- snplib/finalreport/__init__.py,sha256=Yk49x8t-STIfsdP6QLMtaGm1gTj_n-XS8kchPguvW1g,161
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- snplib/finalreport/_finalreport.py,sha256=dE44NsJ5ciGyFCh2LpFncf4LwQDI_-l4LatOPg879Sk,6148
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- snplib/format/__init__.py,sha256=3W_l_sP1u9HV3HWwnsJxPGw9anrVknstqLaJmWQaG0k,261
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- snplib/format/__settings.py,sha256=kyAVZ4tiU61sNr3jQhjXbLXRyBA3pjFfCw3fOfSkY14,289
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- snplib/format/_plink.py,sha256=cjT6PkvDJr8KwvQo76i7_Hm1Og4bASYCDN9G7CHsQ00,10372
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- snplib/format/_snp.py,sha256=oI-V4-_w28aX-VxoimywLDDnX6owhdjLbqt9a54_ouU,3172
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- snplib/parentage/__init__.py,sha256=bN3mWTxmaFQ1qzRtyMLaAoxfomz6jnoWa-kmnJ9q_fE,280
9
- snplib/parentage/_discov.py,sha256=qGlNzpl4xKOWRr6-fi1osylzizgiPO8vCus8VE56nec,3180
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- snplib/parentage/_isagmark.py,sha256=0xi9YhuIpU7zf16HnWw1XIkcQLk4rTNeAeCE-5p9hQE,356
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- snplib/parentage/_verif.py,sha256=VbX46dC4tl4Qeuw65aRg1s6hSn0FI25Hy9-3U_jxmrg,3019
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- snplib/parentage/isag_disc.pl,sha256=XzjcsnO_kwPg4WaE2YMuZXBNHQ9ixi6pg5n2mfGOuJU,14219
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- snplib/parentage/isag_verif.pl,sha256=e_c4YGd5_JXGWqFQwmcxjp6hEkdcqpK_5y5MqJ8J9YY,8254
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- snplib/statistics/__init__.py,sha256=XJFU7mEwAJJ2M187jEkO8rFNYKoxF-g9KF_stS7eFFw,302
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- snplib/statistics/_callrate.py,sha256=yfHxnNVpcDfV3qxZVwrk2RWPgy9dTf7NHWczDUORwtY,1866
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- snplib/statistics/_freq.py,sha256=ZPZBZM3xq9EseOxuMzRVvzkjjFfaaA4ZvF7XI8ctON0,1623
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- snplib/statistics/_snphwe.py,sha256=KcoRGwovMCc53-GJ8VfYs_3ZEHObgt8B0EvrW5nFnmM,3353
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- snplib-1.1.10.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
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- snplib-1.1.10.dist-info/METADATA,sha256=hmE1zLFNhDwwbl03PVupafM1n-NGOV2yKYmKzi1a6lw,2184
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- snplib-1.1.10.dist-info/top_level.txt,sha256=CGCrLXuCSyXPCTwMFQjPxQR7b93FFFft56sAPPun_2g,7
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- snplib-1.1.10.dist-info/RECORD,,