LEFSE_FORMAT_INPUT.PY(1)

💖 NAME 💖

lefse_format_input.py — bestie, this is the tool that figures out the features of organisms, clades, taxonomic units, and genes 🦋

🌸 DESCRIPTION 🌸

okay so, real talk: this is how you run it 👇

usage: lefse_format_input.py [-h] [--output_table OUTPUT_TABLE] [-f {c,r}] [-c [1..n_feats]] [-s [1..n_feats]] [-o float] [-u [1..n_feats]] [-m {f,s}] [-n int] [-biom_c BIOM_CLASS] [-biom_s BIOM_SUBCLASS] INPUT_FILE OUTPUT_FILE

LEfSe formatting modules ✨ — that's the whole vibe of this thing.

🎀 positional arguments:

• INPUT_FILE — the input file, bb. the feature hierarchical level can be specified with | or . — and heads up, those symbols must not be present for any other reason in the input file. no cap, that's a hard requirement 💅
• OUTPUT_FILE — the output file containing the data for LEfSe 👑

🫶 optional arguments:

• -h, --help — show this help message and exit. the classic, iconic, always there for you 🥰
• --output_table OUTPUT_TABLE — the formatted table in txt format 📄
• -f {c,r} — set whether the features are on rows (that's the default) or on columns 🔄
• -c [1..n_feats] — set which feature use as class (default 1) 🌟
• -s [1..n_feats] — set which feature use as subclass (default -1 meaning no subclass) 🧚
• -o float — set the normalization value (default -1.0 meaning no normalization) ⚖️
• -u [1..n_feats] — set which feature use as subject (default -1 meaning no subject) 💫
• -m {f,s} — set the policy to adopt with missing values: f removes the features with missing values, s removes samples with missing values (default f) 💀
• -n int — set the minimum cardinality of each subclass (subclasses with low cardinalities will be grouped together, and if the cardinality is still low, no pairwise comparison will be performed with them) 📊
• -biom_c BIOM_CLASS — For biom input files: Set which feature use as class 🧬
• -biom_s BIOM_SUBCLASS — For biom input files: set which feature use as subclass 🧬

👑 AUTHOR 👑

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. 🫶

aaaand that's the whole page, bestie 💜 this was lefse_format_input.py version 1.1.2, dated September 2021, straight out of the Debian-verse. go format some features, you got this 🌈⭐