MASKPRIMERS.PY(1)

💖 MASKPRIMERS.PY(1) — User Commands 💖

okay bestie, this is the manual page for MASKPRIMERS.PY(1) in the User Commands section, and I'm about to walk you through it 🫶

✨ NAME ✨

okay so MaskPrimers.py is the tool that removes primers and annotates sequences with primer and barcode identifiers 💅

🦋 DESCRIPTION 🦋

here's the usage line, verbatim, so you can copy it straight into your terminal 🌸

usage: MaskPrimers.py [--version] [-h]  ...

the whole vibe is that it removes primers and annotates sequences with primer and barcode identifiers, no cap 🔥

🎀 help 🎀

• --version — pulls up the program's version number and then bounces 👋
• -h, --help — shows the help message and then exits, iconic 💖

🧚 subcommands 🧚

Alignment method is the category these fall under, and here's the lineup 💜

• align — finds primer matches using pairwise local alignment ✨
• score — finds primer matches by scoring primers at a fixed position 🎯
• extract — removes and annotates a fixed sequence region 🫧

📁 output files 📁

• mask-pass — processed reads with successful primer matches, the ones that made it 🍓
• mask-fail — raw reads that failed primer identification 🥀

🏷️ output annotation fields 🏷️

• SEQORIENT — the orientation of the output sequence. It's either F (input) or RC (reverse complement of input) 🔄
• PRIMER — the name of the best primer match 👑
• BARCODE — the sequence preceding the primer match. It only shows up when the --barcode flag is specified, so don't forget that flag 🙈

👑 AUTHOR 👑

Andreas Tille wrote this manpage for the Debian distribution, and it's giving open-source energy: it can be used for any other usage of the program 🫶💅

signing off with MaskPrimers.py 0.6.0 from May 2020 💜✨ stay iconic, bestie 🌈🦋