GLISTQUERY(1)

📦 version 4.0+git20221122.71e6625, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

💖 GLISTQUERY(1) 💖

okay bestie, so this is a page from the GenomeTester user manuals, and it's about a lil tool called glistquery — she's the one who tells you how often your k-mers show up in a list file. let's get into it 🫶

✨ NAME ✨

glistquery — print the frequencies of k-mers in a list file 💅

🌸 SYNOPSIS 🌸

glistquery <INPUTLIST> [OPTIONS]

like, you hand her an <INPUTLIST> and then whatever [OPTIONS] you're feeling, and she goes off. periodt.

🎀 OPTIONS 🎀

  • -v, --version — print version information and exit. she'll tell you who she is and then dip 👋
  • -h, --help — print this usage screen and exit. the classic "help me help you" move 💖
  • -stat — print statistics of the list file and exit. just the stats, no notes, and then she's gone ✨
  • -median — print min/max/median/average and exit. the whole lil stats squad, then exit 📊
  • -q, --query — single query word. one (1) word, that's the vibe 🌸
  • -f, --queryfile — list of query words in a file. when one word isn't enough and you need a whole file of them 🦋
  • -s, --seqfile — FastA/FastQ file. hand her a sequence file and she'll take it from there 🧬
  • -l, --listfile — list file made by glistmaker. this is the list file that glistmaker built, so it's gotta come from there, iykyk 💜
  • -mm, --mismatch NUMBER — specify number of mismatches (default 0, can be used with -d and -dd). so, default is 0 mismatches, and just so you know, it can be used together with -d and -dd 👀
  • -p, --perfectmatch NUMBER — specify number of 3' perfect matches (default 0) ✨
  • -min, --minfreq NUMBER — minimum frequency of the printed words (default 0). sets the floor, bestie, nothing below this gets printed 🍓
  • -max, --maxfreq NUMBER — maximum frequency of the printed words (default MAX_UINT). yes, the default is literally MAX_UINT, she's not even trying to filter anything out by default 😭
  • -all — in case of mismatches prints all found words. like, all of them, no holding back 💀
  • -D — increase debug level. for when you need to know exactly what's going on in there 🔥

🌈 EXAMPLES 🌈

you could find some usage examples in:

/usr/share/doc/genometester/README.GenomeTester4.md

go look, she left them there for you 🥰

👑 SEE ALSO 👑

the whole friend group, fr fr 💕

and that's the whole page bestie!! this one came from GenomeTester, dated 31 May 2018 — so like, she's been iconic for a minute and she's not stopping 💖✨🎀 slay, mwah 🫶

📦 where this page comes from