LogolExec(1)

💖 LogolExec(1) 💖

Bestie, this is the USER COMMANDS page for LogolExec(1), and I am obsessed 🫶 Let me walk you through it.

✨ NAME ✨

Okay so LogolExec is the program that parses a logol grammar and searches for patterns in a sequence 🧚 Main character energy, literally.

✨ SYNOPSIS ✨

LogolExec [-h]

✨ INSTALLATION ✨

Logol needs the Cassiopee Ruby gem 💅 To install it, run:

gem install cassiopee

✨ CONFIGURATION ✨

LogolExec uses a default config file at /etc/logol/logol.properties 🌸 but you can point it at a different one from the command line.

The temporary and results directories must be writable by the user. Ngl, this one is important 😭

By default, /var/lib/logol/results holds the generated results, and /tmp is used as the temporary directory 🦋

✨ OPTIONS ✨

You need at least -m (logol model) or -g (logol grammar), plus -s (input sequence). No skipping these, bestie 🎀

💜 MAIN OPTIONS 💜

• -h — pulls up the list of commands 📋
• -v — tells you the version 🔖
• -conf — lets you specify a configuration file 🗂️
• -s — the sequence file you want to analyse 🧬
• -g — the grammar file you want to analyse 📜
• -m — the model file you want to analyse 🧩
• -check — checks a grammar without running anything 🔍 It requires -g
• -dna — analyses DNA, and it's the default 🧬
• -rna — analyses RNA 🌿
• -protein — analyses protein 🫧
• -max — the maximum number of solutions returned 🔢
• -all — analyses both directions of the sequence ↔️
• -output — the output file name, which must be unique 📁

🌈 OTHER OPTIONS 🌈

• -sequenceID — the position of the sequence in the bank 🍓
• -uid — uses an identifier you define for the query 🪪
• -lmax — the maximum length of a variable 📏
• -maxspacer — the maximum size of a spacer 🫧
• -offset — an offset value added to positions ➕
• -start — the start position on the sequence ▶️
• -end — the end position on the sequence ⏹️
• -noclean — doesn't delete the created files after processing. This is for debugging 🙈
• -enabledups — turns on duplicate result matches. By default, only singletons are kept 👯
• -filter — the filter type, used when -enabledups is not enabled. Allowed types: exact(default),local,local0,global 🪄
• -lmin — the minimum length of a variable, which speeds up parsing 🏃‍♀️
• -c — the maximum size of a match, which speeds up parsing ⚡
• -maxres — the maximum result size of a match, which speeds up parsing 💨

✨ AUTHOR ✨

Olivier Sallou (olivier.sallou (at) irisa.fr) is the legend behind this 👑

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That's the whole tea, bestie 🍵 Version 1.0, September 28, 2011. Now go slay your grammars 💅🎀🦋