TRIMSEQ(1e)

📦 version 6.6.0, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

🎀 NAME 🎀

trimseq — Remove unwanted characters from start and end of sequence(s). She's the main character here, bestie ✂️✨. This is the TRIMSEQ(1e) page from the EMBOSS Manual for Debian, btw 💖.

✨ SYNOPSIS ✨

trimseq -sequence seqall [-window integer] [-percent float]
        [-strict boolean] [-star boolean] -left boolean -right boolean
        -outseq seqoutall

trimseq -help

🦋 DESCRIPTION 🦋

Okay so trimseq is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”) 💖. It is part of the "Edit" command group(s) — yes, group(s), no cap. She's ready to edit your sequences like a boss 👑.

💅 OPTIONS 💅

🌸 Input section 🌸

  • -sequence seqall — your input sequence(s), bestie. The original doesn't say more here, so that's the whole tea 🍓.

🎀 Additional section 🎀

  • -window integer — This determines the size of the region that is considered when deciding whether the percentage of ambiguity is greater than the threshold. A value of 5 means that a region of 5 letters in the sequence is shifted along the sequence from the ends, and trimming is done only if there is a greater or equal percentage of ambiguity than the threshold percentage. Default value: 1 ✨.
  • -percent float — This is the threshold of the percentage ambiguity in the window required in order to trim a sequence. Default value: 100.0 💯.
  • -strict boolean — In nucleic sequences, trim off not only N's and X's, but also the nucleotide IUPAC ambiguity codes M, R, W, S, Y, K, V, H, D and B. In protein sequences, trim off not only X's but also B and Z. Default value: N 🧬.
  • -star boolean — In protein sequences, trim off not only X's, but also the *'s. Default value: N ⭐.

🌈 Advanced section 🌈

  • -left boolean — Default value: Y. The original gives no extra prose here, she's just like that 💛.
  • -right boolean — Default value: Y. Again, no extra description in the original — just the default, bestie 🧡.

🦋 Output section 🦋

  • -outseq seqoutall — where your output sequence(s) go, obviously. No extra notes in the original 💙.

😭 BUGS 😭

Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031) 🐛.

bestie, if something's busted, report it to them, not me 😭.

👀 SEE ALSO 👀

trimseq is fully documented via the tfm(1) system. Go read that if you want the deep lore 📚.

🫶 AUTHOR 🫶

Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org> — Wrote the script used to autogenerate this manual page. Iconic behavior, honestly 👑.

This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself. Respect the license, bestie 💅.

💖 That's the whole page! This was EMBOSS 6.4.0, dated 05/11/2012, and the manual is TRIMSEQ(1e). Stay trimmed, stay iconic, bye! 💖

📦 where this page comes from