SEQMAGICK(1)

💅 SEQMAGICK 💅

okay so bestie, gather round, because seqmagick is here and she is that girl 🌟

seqmagick — Manipulate sequence files. That's the whole vibe. It's a section 1 (User Commands) situation, iykyk.

She's a little utility whose whole thing is exposing the file format conversion powers hiding inside BioPython, but, like, in a convenient way ✨ no cap, that's genuinely the entire pitch.

✨ SYNOPSIS ✨

usage: seqmagick [-h] [-V] [-v] [-q]

       help, convert, info, mogrify, primer-trim, quality-filter,
       extract-ids, backtrans-align ...

🎀 DESCIPTION 🎀

(yes bestie, that's literally how it's spelled in the original — i am not touching it, it's iconic 💀)

Seqmagick is a little utility to expose the file format conversion in BioPython in a convenient way.

that's it. that's the description. short, sweet, does exactly what it says on the tin 🫶

🌸 OPTIONS 🌸

positional arguments: 🦋

These are the moves, the actions, the main character moments:

• help, convert, info, mogrify, primer-trim, quality-filter, extract-ids, backtrans-align — the full lineup, in order, no substitutions 💖

and here's what each one actually does:

• help — Detailed help for actions, using help <action> 👑 like, if you wanna know more about one specific move, you ask her directly.
• convert — Convert between sequence formats. glow up, format edition ✨
• info — Info action. it's giving "tell me about yourself" 🎀
• mogrify — Modify sequence file(s) in place. yes bestie, in place, so she's editing your files right where they live 🙈
• primer-trim — Find a primer sequence in a gapped alignment, trim to amplicon. snipping szn ✂️
• quality-filter — Filter reads based on quality scores. only the good ones get through 💅
• extract-ids — Extract the sequence IDs from a file. just the IDs, nothing extra, she's efficient like that 🍓
• backtrans-align — Given a protein alignment and unaligned nucleotides, align the nucleotides using the protein alignment. Protein and nucleotide sequence files must contain the same number of sequences, in the same order, with the same IDs. okay that last part is a real requirement, not a suggestion — same count, same order, same IDs, or she cannot help you 😭

optional arguments: 🌈

• -h, --help — show this help message and exit. the classic, the icon, the one you type when you're lost 🫶
• -V, --version — Print the version number and exit. who am i? she'll tell you 🦋
• -v, --verbose — Be more verbose. Specify -vv or -vvv for even more. she can be so chatty if you let her, and honestly? obsessed 💬
• -q, --quiet — Suppress output. shhh 🤫 the opposite of the -v energy.

👑 AUTHOR 👑

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. shoutout Andreas, absolute legend, thank you for your service 🫡💖

and that's the whole page bestie!! this one's seqmagick version 0.6.1, dated June 2017, and it lives in section 1 of the manual as SEQMAGICK(1) 🎀 periodt. go forth and manipulate those sequence files, you've got this 🌸🦋✨