LEFSE_RUN.PY(1)

okay bestie, sit down, we're doing LEFSE_RUN.PY(1) together and honestly? it's giving main character energy. it's the man page for lefse_run.py, and by the end of this you're gonna understand it better than the person who wrote it. no cap. 🦋✨

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🎀 NAME 🎀

lefse_run.py — the one that figures out the features of organisms, clades, taxonomic units and genes that actually matter. like, it does the science so you don't have to. periodt. 💅

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💖 DESCRIPTION 💖

here's literally how you call it, verbatim, don't @ me:

usage: lefse_run.py [-h] [-o str] [-a float] [-w float] [-l float]
       [--nlogs int] [--verbose int] [--wilc int] [-r str]
       [--svm_norm int] [-b int] [-e int] [-c int] [-f float] [-s {0,1,2}]
       [--min_c int] [-t str] [-y {0,1}] INPUT_FILE OUTPUT_FILE

this is LEfSe 1.1.01, iconic, obsessed. 👑

🍓 positional arguments

• INPUT_FILE — the input file. your data. the moment. 🌸
• OUTPUT_FILE — the output file, and it's holding the data that the visualization module is gonna eat up later. so you're not just writing a file, you're serving looks to the next step. ✨

🌸 optional arguments

• -h, --help — shows this help message and then exits, like a polite queen. 💅
• -o str — sets the file you export the result to (concise textual form only, bestie, don't get greedy). 🎀
• -a float — sets the alpha value for the Anova test (default 0.05). 🌸
• -w float — sets the alpha value for the Wilcoxon test (default 0.05). 💖
• -l float — sets the threshold on the absolute value of the logarithmic LDA score (default 2.0). ⭐
• --nlogs int — max log ingluence of LDA coeff. that's it, that's the whole description, we move. ✨
• --verbose int — verbose execution (default 0). turn it up if you want the running commentary, iykyk. 🗣️
• --wilc int — whether to perform the Wicoxon step (default 1). yes default, it's doing it. 🦋
• -r str — select LDA or SVM for effect size (default LDA). pick your fighter. 👑
• --svm_norm int — whether to normalize the data in [0,1] for SVM feature waiting (default 1 — strongly suggested, so like... don't be weird about it, leave it on). 🔥
• -b int — sets the number of bootstrap iterations for LDA (default 30). count 'em. 🔢
• -e int — sets whether to perform the wilcoxon test only among the subclasses with the same name (default 0). 🫶
• -c int — sets whether to perform the wilcoxon test ing the Curtis's approach (BETA VERSION) (default 0). 🧚

bestie it literally says BETA VERSION in the docs. it's not me being dramatic, that's just the lore. handle with care. 💀

• -f float — sets the subsampling fraction value for each bootstrap iteration (default 0.66666). yes, all those sixes. 😭
• -s {0,1,2} — sets the multiple testing correction options. 0 = no correction, which is more strict, and yes it's the default; 1 = correction for independent comparisons; 2 = correction for dependent comparison. choose your destiny. 🌈
• --min_c int — minimum number of samples per subclass for performing the wilcoxon test (default 10). 🌸
• -t str — sets the title of the analysis (default is the input file without its extension — cute, it names itself). 🎀
• -y {0,1} — for multiclass tasks: sets whether the test runs in a one-against-one setting (1 — more strict!) or in a one-againstall setting (0 — less strict) (default 0). ⚡

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👑 AUTHOR 👑

This manpage was written by Andreas Tille for the Debian distribution, and can be used for any other usage of the program. we love a legend who documents things. 🫶

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and that's the whole thing bestie, you ate. go run some features. 💖

lefse_run.py 1.1.2 · September 2021 · mwah, stay iconic ✨🎀🦋