winpca 1.3__tar.gz

winpca-1.3/LICENSE

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+MIT License
+
+Copyright (c) 2025 Luka Moritz Blumer
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

winpca-1.3/PKG-INFO

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+Metadata-Version: 2.4
+Name: winpca
+Version: 1.3
+Summary: WinPCA - A package for windowed principal component analysis
+Author-email: Moritz Blumer <lmb215@cam.ac.uk>
+License: MIT License
+        
+        Copyright (c) 2025 Luka Moritz Blumer
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Homepage, https://github.com/MoritzBlumer/winpca
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: scikit-allel
+Requires-Dist: plotly>=6
+Requires-Dist: kaleido>=1
+Requires-Dist: pcangsd>=1.36.4
+Dynamic: license-file
+
+
+# _WinPCA_
+
+A package for windowed principal component analysis.
+WinPCA performs principal component analyses (PCA) in sliding windows along chromosomes. Both hard-called genotypes (input: VCF or TSV) and genotype likelihoods (input: VCF, TSV or BEAGLE) encoding **biallelic SNPs** are accepted. WinPCA uses [scikit-allel](https://scikit-allel.readthedocs.io/en/stable/stats/decomposition.html?highlight=pca) to perform PCAs on genotype data and [PCAngsd](https://github.com/Rosemeis/pcangsd) methods for genotype likelihood (GL, PL) data.
+
+WinPCA can aid the initial exploration of new datasets since no prior grouping of input samples is necessary to visualize genetic structure. It has also been used to [identify chromosome-scale inversions in cichlids and to visualize the recombination landscape in a species cross](https://www.biorxiv.org/content/10.1101/2024.07.28.605452v2.full) (Fig. 2) or to [identify ancestry tracts in a hybrid mouse](https://www.biorxiv.org/content/10.1101/2024.08.31.610610v2.full) (Fig. 6).
+
+![example_pca_plot](assets/example.png)
+<br />
+<br />
+
+
+# Installation
+
+## mamba/conda
+
+Simplest install with mamba or conda:
+```
+mamba install -c conda-forge -c bioconda winpca
+```
+
+## git
+
+### _Dependencies_
+Please ensure to have these dependencies installed and accessible from your current shell environment: Python packages: [numpy](https://anaconda.org/anaconda/numpy), [pandas](https://anaconda.org/anaconda/pandas), [scikit-allel](https://anaconda.org/conda-forge/scikit-allel), [plotly](https://anaconda.org/plotly/plotly):
+```
+mamba install numpy pandas scikit-allel "plotly>=6"
+```
+
+Additionally, to run WinPCA on genotype likelihood (GL/PL) data: [PCAngsd](https://github.com/Rosemeis/pcangsd) (installation instructions included), and to render PNG/PDF/SVG plots, [kaleido](https://anaconda.org/channels/conda-forge/packages/python-kaleido/overview).
+<br />
+<br />
+
+### _Obtain WinPCA_
+```
+git clone https://github.com/MoritzBlumer/winpca.git  # clone github repository
+chmod +x winpca/winpca                                # make exceutable
+```
+<br />
+
+# Quick start
+_Minimal command line to visualize PC 1 along a chromosome (using GT data from a VCF)_:
+<br />
+
+```
+# windowed PCA with default settings (after adding winpca to $PATH)
+winpca pca PREFIX VCF_PATH CHROM_NAME:1-CHROM_SIZE
+
+# make a plot of principal component 1 and color by inversion state
+winpca chromplot PREFIX CHROM_NAME:1-CHROM_SIZE -m METADATA_PATH -g METADATA_COLUMN_NAME
+```
+
+
+_Please refer to the help messages (winpca {method} -h) or to the [wiki](https://github.com/MoritzBlumer/winpca/wiki) for the full documentation, file format specifications, more use cases and a tutorial to produce the above plot._
+
+<br />
+
+
+## Citation
+Blumer LM, Good JM & Durbin R (2025). [WinPCA: A package for windowed principal component analysis](https://doi.org/10.1093/bioinformatics/btaf529). _Bioinformatics_, btaf529.
+
+## Contact
+
+Moritz Blumer: lmb215@cam.ac.uk
+

winpca-1.3/README.md

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+
+# _WinPCA_
+
+A package for windowed principal component analysis.
+WinPCA performs principal component analyses (PCA) in sliding windows along chromosomes. Both hard-called genotypes (input: VCF or TSV) and genotype likelihoods (input: VCF, TSV or BEAGLE) encoding **biallelic SNPs** are accepted. WinPCA uses [scikit-allel](https://scikit-allel.readthedocs.io/en/stable/stats/decomposition.html?highlight=pca) to perform PCAs on genotype data and [PCAngsd](https://github.com/Rosemeis/pcangsd) methods for genotype likelihood (GL, PL) data.
+
+WinPCA can aid the initial exploration of new datasets since no prior grouping of input samples is necessary to visualize genetic structure. It has also been used to [identify chromosome-scale inversions in cichlids and to visualize the recombination landscape in a species cross](https://www.biorxiv.org/content/10.1101/2024.07.28.605452v2.full) (Fig. 2) or to [identify ancestry tracts in a hybrid mouse](https://www.biorxiv.org/content/10.1101/2024.08.31.610610v2.full) (Fig. 6).
+
+![example_pca_plot](assets/example.png)
+<br />
+<br />
+
+
+# Installation
+
+## mamba/conda
+
+Simplest install with mamba or conda:
+```
+mamba install -c conda-forge -c bioconda winpca
+```
+
+## git
+
+### _Dependencies_
+Please ensure to have these dependencies installed and accessible from your current shell environment: Python packages: [numpy](https://anaconda.org/anaconda/numpy), [pandas](https://anaconda.org/anaconda/pandas), [scikit-allel](https://anaconda.org/conda-forge/scikit-allel), [plotly](https://anaconda.org/plotly/plotly):
+```
+mamba install numpy pandas scikit-allel "plotly>=6"
+```
+
+Additionally, to run WinPCA on genotype likelihood (GL/PL) data: [PCAngsd](https://github.com/Rosemeis/pcangsd) (installation instructions included), and to render PNG/PDF/SVG plots, [kaleido](https://anaconda.org/channels/conda-forge/packages/python-kaleido/overview).
+<br />
+<br />
+
+### _Obtain WinPCA_
+```
+git clone https://github.com/MoritzBlumer/winpca.git  # clone github repository
+chmod +x winpca/winpca                                # make exceutable
+```
+<br />
+
+# Quick start
+_Minimal command line to visualize PC 1 along a chromosome (using GT data from a VCF)_:
+<br />
+
+```
+# windowed PCA with default settings (after adding winpca to $PATH)
+winpca pca PREFIX VCF_PATH CHROM_NAME:1-CHROM_SIZE
+
+# make a plot of principal component 1 and color by inversion state
+winpca chromplot PREFIX CHROM_NAME:1-CHROM_SIZE -m METADATA_PATH -g METADATA_COLUMN_NAME
+```
+
+
+_Please refer to the help messages (winpca {method} -h) or to the [wiki](https://github.com/MoritzBlumer/winpca/wiki) for the full documentation, file format specifications, more use cases and a tutorial to produce the above plot._
+
+<br />
+
+
+## Citation
+Blumer LM, Good JM & Durbin R (2025). [WinPCA: A package for windowed principal component analysis](https://doi.org/10.1093/bioinformatics/btaf529). _Bioinformatics_, btaf529.
+
+## Contact
+
+Moritz Blumer: lmb215@cam.ac.uk
+

winpca-1.3/modules/__init__.py

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+"""
+WinPCA modules.
+"""
+
+
+## METADATA
+__author__ = 'Moritz Blumer, 2024'
+__version__ = '1.3'
+__email__ = 'lmb215@cam.ac.uk'
+
+
+## IMPORT CONFIG
+from . import config