SQUIZZ(1)

📦 version 0.99d, in debian bookworm, ubuntu jammy, ubuntu noble

✨ SQUIZZ 💅 (section 1 of the User Manuals, bestie)

okay so this is the manual page for squizz, aka the little legend that goes by squizz - Sequence format checker" 4 🫶 (yes that quote mark and that 4 are literally in the name line, i don't make the rules, i just report them 💀)

🌈 SYNOPSIS 🌈

squizz [-AShlnsv] [-c format] [-f format] file

that's the whole vibe. flags go in, a file comes out the other end, everyone eats. 🍓

💖 OPTIONS 💖

Following command line options are allowed (and yes, we're doing all of them, no skipping, no cap):

  • -A — restrict detection/verification to alignment formats only. heads up though: this conflicts with -S so pick a lane bestie 😭
  • -S — restrict detection/verification to sequence formats only. same energy, opposite direction: this conflicts with -A.
  • -c format — convert whatever sequence/alignment got detected into format. cute, except plot twist: this option implies strict alignment checking. so it's strict whether you asked or not 💅
  • -f format — assume the input format is format. do not try to detect anything, just verify that the given one is actually correct. trust but verify, fr fr.
  • -h — display the help message and exit. classic. iconic.
  • -l — list all supported formats. a whole menu, slay.
  • -n — count and report detected entries. ⚠️ but it's picky: this one is only available when the detection is restricted to a single type (so, with the -A or -S options) and strict checks are enabled (so, without the -s option). conditions, bestie. conditions.
  • -s — disable strict format checks (which are enabled by default). living dangerously, i respect it 🙈
  • -v — display version information and exit.

🦋 DESCRIPTION 🦋

squizz is a sequence format file checker — that's the main character job — but it has some conversion capabilities too. multi-talented, honestly.

squizz can detect the most common sequence and alignment formats :

  • CODATA, EMBL, FASTA, GCG, GDE, GENBANK, IG, NBRF (pir), RAW, and SWISSPROT.
  • CLUSTAL, FASTA, MSF, NEXUS, PHYLIP (interleaved and sequential) and STOCKHOLM.

(yes FASTA shows up in both lists. she contains multitudes. 🧚)

squizz can do some conversions too, if the format the input format is supported. Only 3 types are available : sequence to sequence, alignment to alignment, and alignment to sequence (the last one, sequence to alignment, require multiple alignments algorithms and cannot be handled with formatting tools). so that fourth one? not a formatting tool's problem. not our problem. moving on 💅

Strict format checks validate the previously detected objects, by making some sanity checks:

  • sequence strings must exists.
  • alignment is made of more than one sequence.
  • alignment sequence strings must have the same length.
  • alignment sequence names must exists, and be unique.

that's the vibe check right there. if any of those flop, the format does not pass. periodt. 👑

🌸 SEE ALSO 🌸

go read those too, they're part of the lore.

💜 AUTHOR 💜

Nicolas Joly (njoly@pasteur.fr), Institut Pasteur.

ok that's the whole page, you understood all of it, i'm so proud of you 🥹🫶 go check some formats bestie, you're gonna ate 💖

this was the User Manuals SQUIZZ(1) page, dated 2015-09-21, brought to you by the lovely folks on Unix. mwah. 💋

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