Evan Rees

Incorrect download_eggnog_data.py arguments

2

Hello, I recently came across your tool and wanted to give it a try. I've successfully installed `biobakery_workflows` using conda via the conda command: `conda install -c biobakery biobakery_workflows`. Next...

Fix Biopython deprecation warning: ```console /usr/share/miniconda/envs/autometa/lib/python3.8/site-packages/Bio/SeqUtils/__init__.py:144: BiopythonDeprecationWarning: GC is deprecated; please use gc_fraction instead. ``` Instead of `SeqUtils.GC` use `SeqUtils.gc_fraction` Found in logs here: https://github.com/KwanLab/Autometa/actions/runs/4994350221/jobs/8944784711?pr=325 `SeqUtils.gc_fraction` implementation is here: https://github.com/biopython/biopython/blob/8293b7382081b8f6cc135638a956a7736633115e/Bio/SeqUtils/__init__.py#L48-L136...

Migrate documentation from reStructuredText to MyST Markdown

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1. Convert documentation to markdown format for ability to copy code blocks by simply clicking the copy button that appears in the code block rather than having to drag the...

Prior to [dataclasses](https://docs.python.org/3/library/dataclasses.html "python dataclasses docs") availability within the python standard library, `attrs` was used. This may be replaced now to reduce the requirements list. https://github.com/KwanLab/Autometa/blob/baf61c04dddf5b33bb825dba2841de1e38dffefe/autometa/binning/unclustered_recruitment.py#L76-L86 https://github.com/KwanLab/Autometa/blob/baf61c04dddf5b33bb825dba2841de1e38dffefe/make_test_data.py#L99-L100 https://github.com/KwanLab/Autometa/blob/baf61c04dddf5b33bb825dba2841de1e38dffefe/autometa-env.yml#L7 This is...

Replace prodigal subprocess functions with cython bindings python interface to prodigal using [pyrodigal](https://github.com/althonos/pyrodigal) This repo offers [a number of enhancements](https://github.com/althonos/pyrodigal#%EF%B8%8F-overview) Example usage with biopython is also outlined - [example :memo::link:](https://github.com/althonos/pyrodigal#-biopython)

From [scikit-learn clustering docs](https://scikit-learn.org/stable/modules/clustering.html#dbscan), DBSCAN's memory consumption may be optimized: > #### Memory consumption for large sample sizes > > This implementation is by default not memory efficient because it...

Prevent edge case where MAG completeness will be incorrectly computed. This occurs when all single-copy markers are _not_ represented in the respective metagenome assembly. This causes the `reference_markers_count` value to...

Animations in methods documentation

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# Autometa Methods Documentation Video Series This is a series of videos with voiceovers visualizing describing Autometa methods with visual aides generated by [manim](https://www.manim.community/) animations. ## 📝:movie_camera: :speaker:🎨 Scripts /...

Autometa Logo

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:art: Logo for Autometa :art: Ideas, Inspirations and Suggestions: - Mosaic of bacteria - Something similar to the style of a Ishihara Test (color blind test) - Container of DNA...

I think it may be helpful to throw an example into Jupyter notebook and link to it (or https://docs.readthedocs.io/en/stable/guides/jupyter.html) Especially since the tutorial jumps around between running things on command...