RAPTOR-UPGRADE(1)

✨ RAPTOR-UPGRADE(1) ✨

okay bestie, listen up 💖 this is the manual page for raptor-upgrade, which lives in section 1 of the manual. She's a fast and space-efficient pre-filter for querying very large collections of nucleotide sequences. That's the whole name line, we're not being weird about it, we're just folding it in here at the top like the little intro it deserves. 🦋

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🌸 NAME 🌸

Raptor-upgrade — a fast and space-efficient pre-filter for querying very large collections of nucleotide sequences. 🧬✨

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💅 SYNOPSIS 💅

raptor upgrade --input <file> --output <file> [--fpr <number>|--bins
<file>]

That's the vibe check: --input and --output are the moment, and then you pick either --fpr or --bins for the false positive rate situation. Not both. Never both. Mutual exclusivity is real. 💀

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👑 DESCRIPTION 👑

So like, this tool upgrades a Raptor index created with Raptor 2.0 to be compatible with Raptor 3.0. Glow-up era. 🔥

The only new parameter you need is the false positive rate. And bestie, the false positive rate affects the search results, so this is not a whatever parameter, it's a main character parameter. 🎀

You can get it done in three different ways:

1. Pass the false positive rate via --fpr.
2. The false positive rate can be automatically determined if the paths of the files used to build the index are still available.
3. Pass a file containing the path to the original files, one line per file. The false positive rate can then be automatically determined. The order of the files does not matter. The file with the most k-mers will determine the false positive rate. 👑

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✨ OPTIONS ✨

• --fpr (double) — The false positive rate. Mutually exclusive with --bins. Default: None. Value must be in range [0.000000,1.000000]. So like, keep it inside the range, she's not flexible on that. 🙈
• --bins (std::filesystem::path) — File containing one file per line per bin. Mutually exclusive with --fpr. Default: None. The input file must exist and read permissions must be granted. No read permissions = no vibes. 😭
• --input (std::filesystem::path) — The index to upgrade. Parts: Without suffix _0. FYI on the _0 part, iykyk. 💅
• --output (std::filesystem::path) — Path to new index. Fresh index, fresh era. ✨

🫶 Common options 🫶

• -h, --help — Prints the help page.
• -hh, --advanced-help — Prints the help page including advanced options.
• --version — Prints the version information.
• --copyright — Prints the copyright/license information.
• --export-help (std::string) — Export the help page information. Value must be one of [html, man, ctd, cwl]. Pick one, she's not taking anything else. 🌈

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🎀 EXAMPLES 🎀

Here's the group chat receipts, all three of them so you literally cannot get it wrong:

raptor upgrade --input old.index --output new.index

raptor upgrade --input old.index --output new.index --fpr 0.05

raptor upgrade --input old.index --output new.index --bins bins.list

Ate. No notes. 💅

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💜 VERSION 💜

• Last update: Unavailable
• Raptor-upgrade version: 3.0.1 (commit unavailable)
• Sharg version: 1.1.1
• SeqAn version: 3.4.0

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🔗 URL 🔗

https://github.com/seqan/raptor — that's the house. 🏠✨

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⭐ LEGAL ⭐

• Raptor-upgrade Copyright: BSD 3-Clause License
• Author: Enrico Seiler
• Contact: enrico.seiler@fu-berlin.de
• SeqAn Copyright: 2006-2023 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.
• In your academic works please cite: Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences; Enrico Seiler, Svenja Mehringer, Mitra Darvish, Etienne Turc, and Knut Reinert; iScience 2021 24 (7): 102782. doi: https://doi.org/10.1016/j.isci.2021.102782
• For full copyright and/or warranty information see --copyright.

Please cite her in your academic works bestie, that's just polite. 🥺 And if you want the full copyright and/or warranty tea, run --copyright.

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okay that's the whole page, and for the cute sign-off: this is raptor-upgrade 3.0.1 (commit unavailable), dated Unavailable, and she's serving RAPTOR-UPGRADE(1) energy the whole way through. Periodt. 💖🦋🌸