XTRACTORE(1)

📦 version 0.16.0, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 XTRACTORE — the manual page, but make it a group chat 💖

okay bestie, so xtractore is the girl who extracts sequences that correspond to annotated features from the sequence file you hand her. that's it, that's the job. she takes your annotations, she takes your sequences, she matches them up. iconic behaviour honestly 🦋

✨ SYNOPSIS ✨

xtractore [options] features.gff3 sequences.fasta

like. give her the options, the features.gff3, and the sequences.fasta, in that order. she's not complicated, she just has standards. 💅

🌸 DESCRIPTION 🌸

she reads your features.gff3, she reads your sequences.fasta, and she pulls out the sequences that line up with the annotated features. that's the whole vibe. no cap.

🎀 Options

here's every single flag, and yes i mean every single one, we're not skipping any, this is a full send ✨

  • -d, --debug — prints debugging output. messy on purpose, but it's the good kind of messy. 🔍
  • -h, --help — prints this help message and then exits. she's helpful like that. 🫶
  • -i, --idfile: FILE — a FILE containing a list of feature IDs, one per line with no spaces. if you provide it, only the features whose IDs show up in this file get extracted. it's giving guest list. 👑
  • -o, --outfile: FILE — the FILE where the output sequences get written. default is the terminal (stdout), so if you don't say anything she'll just say it out loud. 🗣️
  • -t, --type: STRING — the feature type to extract. you can use this one multiple times to extract features of multiple types. stack them, bestie, she can handle it. 🌈
  • -v, --version — prints the version number and exits. short and sweet. ⭐
  • -V, --verbose — prints verbose warning and error messages. so when something goes sideways, she tells you everything. 😭
  • -w, --width: INT — the width of each line of sequence in the Fasta output. default is 80. set it to 0 for no formatting at all — raw, unformatted, feral. 🍓
ngl if you forget which flag does what, -h is right there and she will never judge you for asking. 💖

xtractore 0.15.1 — born January 2016 and still slaying. this has been your user-commands manual page for xtractore, and honestly? she ate. 💅✨🎀

📦 where this page comes from