snplib 1.0.7__tar.gz → 1.0.8__tar.gz
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.
- snplib-1.0.8/.github/workflows/linux.yml +34 -0
- snplib-1.0.8/.github/workflows/macos.yml +34 -0
- snplib-1.0.8/.github/workflows/windows.yml +34 -0
- snplib-1.0.8/.gitignore +25 -0
- snplib-1.0.8/.readthedocs.yaml +37 -0
- {snplib-1.0.7 → snplib-1.0.8}/LICENSE +674 -674
- {snplib-1.0.7/src/snplib.egg-info → snplib-1.0.8}/PKG-INFO +80 -97
- {snplib-1.0.7 → snplib-1.0.8}/README.md +59 -75
- snplib-1.0.8/__init__.py +0 -0
- snplib-1.0.8/docs/Makefile +20 -0
- snplib-1.0.8/docs/_build/doctrees/environment.pickle +0 -0
- snplib-1.0.8/docs/_build/doctrees/examples.doctree +0 -0
- snplib-1.0.8/docs/_build/doctrees/index.doctree +0 -0
- snplib-1.0.8/docs/_build/doctrees/install.doctree +0 -0
- snplib-1.0.8/docs/_build/doctrees/intro.doctree +0 -0
- snplib-1.0.8/docs/_build/doctrees/modules.doctree +0 -0
- snplib-1.0.8/docs/_build/doctrees/snplib.doctree +0 -0
- snplib-1.0.8/docs/_build/doctrees/snplib.finalreport.doctree +0 -0
- snplib-1.0.8/docs/_build/doctrees/snplib.format.doctree +0 -0
- snplib-1.0.8/docs/_build/doctrees/snplib.parentage.doctree +0 -0
- snplib-1.0.8/docs/_build/doctrees/snplib.statistics.doctree +0 -0
- snplib-1.0.8/docs/_build/doctrees/usage.doctree +0 -0
- snplib-1.0.8/docs/_build/html/.buildinfo +4 -0
- snplib-1.0.8/docs/_build/html/_modules/index.html +113 -0
- snplib-1.0.8/docs/_build/html/_modules/snplib/finalreport/_finalreport.html +368 -0
- snplib-1.0.8/docs/_build/html/_modules/snplib/format/_plink.html +422 -0
- snplib-1.0.8/docs/_build/html/_modules/snplib/format/_snp.html +233 -0
- snplib-1.0.8/docs/_build/html/_modules/snplib/parentage/_discov.html +213 -0
- snplib-1.0.8/docs/_build/html/_modules/snplib/parentage/_isagmark.html +126 -0
- snplib-1.0.8/docs/_build/html/_modules/snplib/parentage/_verif.html +202 -0
- snplib-1.0.8/docs/_build/html/_modules/snplib/statistics/_callrate.html +167 -0
- snplib-1.0.8/docs/_build/html/_modules/snplib/statistics/_freq.html +178 -0
- snplib-1.0.8/docs/_build/html/_modules/snplib/statistics/_snphwe.html +243 -0
- snplib-1.0.8/docs/_build/html/_sources/examples.rst.txt +647 -0
- snplib-1.0.8/docs/_build/html/_sources/index.rst.txt +23 -0
- snplib-1.0.8/docs/_build/html/_sources/install.rst.txt +26 -0
- snplib-1.0.8/docs/_build/html/_sources/intro.rst.txt +15 -0
- snplib-1.0.8/docs/_build/html/_sources/modules.rst.txt +7 -0
- snplib-1.0.8/docs/_build/html/_sources/snplib.finalreport.rst.txt +9 -0
- snplib-1.0.8/docs/_build/html/_sources/snplib.format.rst.txt +10 -0
- snplib-1.0.8/docs/_build/html/_sources/snplib.parentage.rst.txt +12 -0
- snplib-1.0.8/docs/_build/html/_sources/snplib.rst.txt +12 -0
- snplib-1.0.8/docs/_build/html/_sources/snplib.statistics.rst.txt +13 -0
- snplib-1.0.8/docs/_build/html/_sources/usage.rst.txt +26 -0
- snplib-1.0.8/docs/_build/html/_static/_sphinx_javascript_frameworks_compat.js +123 -0
- snplib-1.0.8/docs/_build/html/_static/basic.css +925 -0
- snplib-1.0.8/docs/_build/html/_static/css/badge_only.css +1 -0
- snplib-1.0.8/docs/_build/html/_static/css/fonts/Roboto-Slab-Bold.woff +0 -0
- snplib-1.0.8/docs/_build/html/_static/css/fonts/Roboto-Slab-Bold.woff2 +0 -0
- snplib-1.0.8/docs/_build/html/_static/css/fonts/Roboto-Slab-Regular.woff +0 -0
- snplib-1.0.8/docs/_build/html/_static/css/fonts/Roboto-Slab-Regular.woff2 +0 -0
- snplib-1.0.8/docs/_build/html/_static/css/fonts/fontawesome-webfont.eot +0 -0
- snplib-1.0.8/docs/_build/html/_static/css/fonts/fontawesome-webfont.svg +2671 -0
- snplib-1.0.8/docs/_build/html/_static/css/fonts/fontawesome-webfont.ttf +0 -0
- snplib-1.0.8/docs/_build/html/_static/css/fonts/fontawesome-webfont.woff +0 -0
- snplib-1.0.8/docs/_build/html/_static/css/fonts/fontawesome-webfont.woff2 +0 -0
- snplib-1.0.8/docs/_build/html/_static/css/fonts/lato-bold-italic.woff +0 -0
- snplib-1.0.8/docs/_build/html/_static/css/fonts/lato-bold-italic.woff2 +0 -0
- snplib-1.0.8/docs/_build/html/_static/css/fonts/lato-bold.woff +0 -0
- snplib-1.0.8/docs/_build/html/_static/css/fonts/lato-bold.woff2 +0 -0
- snplib-1.0.8/docs/_build/html/_static/css/fonts/lato-normal-italic.woff +0 -0
- snplib-1.0.8/docs/_build/html/_static/css/fonts/lato-normal-italic.woff2 +0 -0
- snplib-1.0.8/docs/_build/html/_static/css/fonts/lato-normal.woff +0 -0
- snplib-1.0.8/docs/_build/html/_static/css/fonts/lato-normal.woff2 +0 -0
- snplib-1.0.8/docs/_build/html/_static/css/theme.css +4 -0
- snplib-1.0.8/docs/_build/html/_static/doctools.js +156 -0
- snplib-1.0.8/docs/_build/html/_static/documentation_options.js +13 -0
- snplib-1.0.8/docs/_build/html/_static/file.png +0 -0
- snplib-1.0.8/docs/_build/html/_static/jquery.js +2 -0
- snplib-1.0.8/docs/_build/html/_static/js/badge_only.js +1 -0
- snplib-1.0.8/docs/_build/html/_static/js/html5shiv-printshiv.min.js +4 -0
- snplib-1.0.8/docs/_build/html/_static/js/html5shiv.min.js +4 -0
- snplib-1.0.8/docs/_build/html/_static/js/theme.js +1 -0
- snplib-1.0.8/docs/_build/html/_static/language_data.js +199 -0
- snplib-1.0.8/docs/_build/html/_static/logo.png +0 -0
- snplib-1.0.8/docs/_build/html/_static/minus.png +0 -0
- snplib-1.0.8/docs/_build/html/_static/plus.png +0 -0
- snplib-1.0.8/docs/_build/html/_static/pygments.css +75 -0
- snplib-1.0.8/docs/_build/html/_static/searchtools.js +574 -0
- snplib-1.0.8/docs/_build/html/_static/sphinx_highlight.js +154 -0
- snplib-1.0.8/docs/_build/html/examples.html +725 -0
- snplib-1.0.8/docs/_build/html/genindex.html +352 -0
- snplib-1.0.8/docs/_build/html/index.html +143 -0
- snplib-1.0.8/docs/_build/html/install.html +141 -0
- snplib-1.0.8/docs/_build/html/intro.html +126 -0
- snplib-1.0.8/docs/_build/html/modules.html +127 -0
- snplib-1.0.8/docs/_build/html/objects.inv +0 -0
- snplib-1.0.8/docs/_build/html/py-modindex.html +144 -0
- snplib-1.0.8/docs/_build/html/search.html +124 -0
- snplib-1.0.8/docs/_build/html/searchindex.js +1 -0
- snplib-1.0.8/docs/_build/html/snplib.finalreport.html +265 -0
- snplib-1.0.8/docs/_build/html/snplib.format.html +407 -0
- snplib-1.0.8/docs/_build/html/snplib.html +155 -0
- snplib-1.0.8/docs/_build/html/snplib.parentage.html +230 -0
- snplib-1.0.8/docs/_build/html/snplib.statistics.html +245 -0
- snplib-1.0.8/docs/_build/html/usage.html +135 -0
- snplib-1.0.8/docs/conf.py +56 -0
- snplib-1.0.8/docs/examples.rst +647 -0
- snplib-1.0.8/docs/index.rst +23 -0
- snplib-1.0.8/docs/install.rst +26 -0
- snplib-1.0.8/docs/intro.rst +15 -0
- snplib-1.0.8/docs/logo.png +0 -0
- snplib-1.0.8/docs/make.bat +35 -0
- snplib-1.0.8/docs/modules.rst +7 -0
- snplib-1.0.8/docs/snplib.finalreport.rst +9 -0
- snplib-1.0.8/docs/snplib.format.rst +10 -0
- snplib-1.0.8/docs/snplib.parentage.rst +12 -0
- snplib-1.0.8/docs/snplib.rst +12 -0
- snplib-1.0.8/docs/snplib.statistics.rst +13 -0
- snplib-1.0.8/docs/usage.rst +26 -0
- snplib-1.0.8/iconlib.png +0 -0
- {snplib-1.0.7 → snplib-1.0.8}/pyproject.toml +44 -32
- snplib-1.0.8/requirements.txt +14 -0
- {snplib-1.0.7 → snplib-1.0.8}/setup.cfg +4 -4
- {snplib-1.0.7 → snplib-1.0.8}/src/snplib/__init__.py +8 -8
- {snplib-1.0.7 → snplib-1.0.8}/src/snplib/finalreport/__init__.py +7 -7
- {snplib-1.0.7 → snplib-1.0.8}/src/snplib/finalreport/_finalreport.py +251 -251
- {snplib-1.0.7 → snplib-1.0.8}/src/snplib/format/__init__.py +19 -19
- {snplib-1.0.7 → snplib-1.0.8}/src/snplib/format/__settings.py +7 -7
- {snplib-1.0.7 → snplib-1.0.8}/src/snplib/format/_plink.py +305 -305
- {snplib-1.0.7 → snplib-1.0.8}/src/snplib/format/_snp.py +113 -113
- {snplib-1.0.7 → snplib-1.0.8}/src/snplib/parentage/__init__.py +15 -15
- {snplib-1.0.7 → snplib-1.0.8}/src/snplib/parentage/_discov.py +102 -102
- {snplib-1.0.7 → snplib-1.0.8}/src/snplib/parentage/_isagmark.py +15 -15
- {snplib-1.0.7 → snplib-1.0.8}/src/snplib/parentage/_verif.py +91 -91
- snplib-1.0.8/src/snplib/parentage/isag_disc.pl +0 -0
- snplib-1.0.8/src/snplib/parentage/isag_verif.pl +0 -0
- {snplib-1.0.7 → snplib-1.0.8}/src/snplib/statistics/__init__.py +16 -16
- {snplib-1.0.7 → snplib-1.0.8}/src/snplib/statistics/_callrate.py +59 -59
- {snplib-1.0.7 → snplib-1.0.8}/src/snplib/statistics/_freq.py +67 -67
- {snplib-1.0.7 → snplib-1.0.8}/src/snplib/statistics/_snphwe.py +132 -132
- {snplib-1.0.7 → snplib-1.0.8/src/snplib.egg-info}/PKG-INFO +80 -97
- snplib-1.0.8/src/snplib.egg-info/SOURCES.txt +183 -0
- {snplib-1.0.7 → snplib-1.0.8}/src/snplib.egg-info/requires.txt +0 -1
- snplib-1.0.8/tests/__init__.py +0 -0
- {snplib-1.0.7/src/snplib/finalreport/tests → snplib-1.0.8/tests/finalreport}/__init__.py +7 -7
- snplib-1.0.8/tests/finalreport/files/fr/file1.txt +28 -0
- snplib-1.0.8/tests/finalreport/files/fr/file1.xlsx +0 -0
- snplib-1.0.8/tests/finalreport/files/fr/file2.txt +21 -0
- snplib-1.0.8/tests/finalreport/files/fr/file2.xlsx +0 -0
- snplib-1.0.8/tests/finalreport/files/fr/file3.txt +10 -0
- snplib-1.0.8/tests/finalreport/files/fr/file3.xlsx +0 -0
- snplib-1.0.8/tests/finalreport/files/fr/file4.txt +16 -0
- snplib-1.0.8/tests/finalreport/files/fr/file5.txt +0 -0
- snplib-1.0.8/tests/finalreport/files/fr/file5.xlsx +0 -0
- snplib-1.0.8/tests/finalreport/files/fr/file6.txt +28 -0
- snplib-1.0.8/tests/finalreport/files/fr/file6.xlsx +0 -0
- snplib-1.0.8/tests/finalreport/files/fr/file7.txt +28 -0
- snplib-1.0.8/tests/finalreport/files/fr/file7.xlsx +0 -0
- {snplib-1.0.7/src/snplib/finalreport/tests → snplib-1.0.8/tests/finalreport}/test_finalreport.py +215 -215
- {snplib-1.0.7/src/snplib/format/tests → snplib-1.0.8/tests/format}/__init__.py +7 -7
- snplib-1.0.8/tests/format/files/fplink/fam/file.pl +0 -0
- snplib-1.0.8/tests/format/files/fplink/fam/file2.pl +0 -0
- snplib-1.0.8/tests/format/files/fplink/fam/file3.pl +0 -0
- snplib-1.0.8/tests/format/files/fplink/fam/file4.pl +0 -0
- snplib-1.0.8/tests/format/files/fplink/lgen/file.pl +0 -0
- snplib-1.0.8/tests/format/files/fplink/map/file_bovinesnp50.csv +31 -0
- snplib-1.0.8/tests/format/files/fplink/ped/file.pl +0 -0
- snplib-1.0.8/tests/format/files/fplink/ped/file2.pl +0 -0
- snplib-1.0.8/tests/format/files/fplink/ped/file3.pl +0 -0
- snplib-1.0.8/tests/format/files/fplink/ped/file4.pl +0 -0
- snplib-1.0.8/tests/format/files/fsnp/file1.txt +35 -0
- snplib-1.0.8/tests/format/files/fsnp/file2.txt +35 -0
- {snplib-1.0.7/src/snplib/format/tests → snplib-1.0.8/tests/format}/test_plink_fam.py +121 -121
- {snplib-1.0.7/src/snplib/format/tests → snplib-1.0.8/tests/format}/test_plink_lgen.py +106 -106
- {snplib-1.0.7/src/snplib/format/tests → snplib-1.0.8/tests/format}/test_plink_map.py +42 -42
- {snplib-1.0.7/src/snplib/format/tests → snplib-1.0.8/tests/format}/test_plink_ped.py +136 -136
- {snplib-1.0.7/src/snplib/format/tests → snplib-1.0.8/tests/format}/test_snp.py +128 -128
- {snplib-1.0.7/src/snplib/parentage/tests → snplib-1.0.8/tests/parentage}/__init__.py +7 -7
- snplib-1.0.8/tests/parentage/data/parentage_test_disc.csv +623 -0
- snplib-1.0.8/tests/parentage/data/parentage_test_verf.csv +245 -0
- {snplib-1.0.7/src/snplib/parentage/tests → snplib-1.0.8/tests/parentage}/test_discov.py +164 -164
- {snplib-1.0.7/src/snplib/parentage/tests → snplib-1.0.8/tests/parentage}/test_verif.py +160 -160
- {snplib-1.0.7/src/snplib/statistics/tests → snplib-1.0.8/tests/statistics}/__init__.py +7 -7
- snplib-1.0.8/tests/statistics/data/cr/file_cra.pl +0 -0
- snplib-1.0.8/tests/statistics/data/cr/file_crm.pl +0 -0
- snplib-1.0.8/tests/statistics/data/freq/etalon.txt +8 -0
- snplib-1.0.8/tests/statistics/data/freq/file.pl +0 -0
- {snplib-1.0.7/src/snplib/statistics/tests → snplib-1.0.8/tests/statistics}/test_callrate.py +171 -171
- {snplib-1.0.7/src/snplib/statistics/tests → snplib-1.0.8/tests/statistics}/test_freq_allele.py +87 -87
- {snplib-1.0.7/src/snplib/statistics/tests → snplib-1.0.8/tests/statistics}/test_freq_maf.py +17 -17
- {snplib-1.0.7/src/snplib/statistics/tests → snplib-1.0.8/tests/statistics}/test_hwe_t.py +41 -41
- {snplib-1.0.7/src/snplib/statistics/tests → snplib-1.0.8/tests/statistics}/test_snphwe.py +41 -41
- snplib-1.0.7/src/snplib.egg-info/SOURCES.txt +0 -40
- {snplib-1.0.7 → snplib-1.0.8}/src/snplib.egg-info/dependency_links.txt +0 -0
- {snplib-1.0.7 → snplib-1.0.8}/src/snplib.egg-info/top_level.txt +0 -0
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|
+
- name: Test with pytest
|
34
|
+
run: pytest
|
snplib-1.0.8/.gitignore
ADDED
@@ -0,0 +1,25 @@
|
|
1
|
+
/.venv
|
2
|
+
|
3
|
+
*.bz2
|
4
|
+
*.jpg
|
5
|
+
*.log
|
6
|
+
*.html
|
7
|
+
*.rar
|
8
|
+
*.zip
|
9
|
+
*.txt
|
10
|
+
*.csv
|
11
|
+
*.npz
|
12
|
+
*.xlsx
|
13
|
+
*.7z
|
14
|
+
*.ipynb
|
15
|
+
*.docx
|
16
|
+
|
17
|
+
!requirements.txt
|
18
|
+
!/tests/*/**
|
19
|
+
!/docs/*/**
|
20
|
+
|
21
|
+
*.idea*
|
22
|
+
*__pycache__*
|
23
|
+
*.pytest_cache*
|
24
|
+
*.ipynb_checkpoints*
|
25
|
+
|
@@ -0,0 +1,37 @@
|
|
1
|
+
# Read the Docs configuration file for Sphinx projects
|
2
|
+
# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
|
3
|
+
|
4
|
+
# Required
|
5
|
+
version: 2
|
6
|
+
|
7
|
+
# Set the OS, Python version and other tools you might need
|
8
|
+
build:
|
9
|
+
os: ubuntu-22.04
|
10
|
+
tools:
|
11
|
+
python: "3.11"
|
12
|
+
# You can also specify other tool versions:
|
13
|
+
# nodejs: "20"
|
14
|
+
# rust: "1.70"
|
15
|
+
# golang: "1.20"
|
16
|
+
|
17
|
+
# Build documentation in the "docs/" directory with Sphinx
|
18
|
+
sphinx:
|
19
|
+
builder: html
|
20
|
+
configuration: docs/conf.py
|
21
|
+
fail_on_warning: true
|
22
|
+
# You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
|
23
|
+
# builder: "dirhtml"
|
24
|
+
# Fail on all warnings to avoid broken references
|
25
|
+
# fail_on_warning: true
|
26
|
+
|
27
|
+
# Optionally build your docs in additional formats such as PDF and ePub
|
28
|
+
# formats:
|
29
|
+
# - pdf
|
30
|
+
# - epub
|
31
|
+
|
32
|
+
# Optional but recommended, declare the Python requirements required
|
33
|
+
# to build your documentation
|
34
|
+
# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
|
35
|
+
python:
|
36
|
+
install:
|
37
|
+
- requirements: requirements.txt
|