MASKSEQ(1e)

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

💅 MASKSEQ(1e) — the EMBOSS manual, but make it make sense

okay so bestie, you found yourself in the 1e section of the EMBOSS Manual for Debian, and the page you're reading is maskseq. Let's get into it 🫶

✨ NAME ✨

maskseq — write a sequence with masked regions 🎭

🌸 SYNOPSIS 🌸

maskseq -sequence sequence -regions range [-tolower toggle]
        -maskchar string -outseq seqout

maskseq -help

🦋 DESCRIPTION 🦋

maskseq is a command line program from EMBOSS, aka “the European Molecular Biology Open Software Suite”. It lives in the "Edit" command group(s), so it's giving ✨sequence-glow-up✨ energy.

👑 OPTIONS 👑

💖 Input section

  • -sequence sequence — yeah, that's your input sequence, bestie. The one we're about to dress up.

🎀 Required section

  • -regions range — the regions you wanna mask. A set of regions = a set of pairs of positions. The positions are integers. They get separated by any non-digit, non-alpha character (so basically, whatever punctuation you vibe with works). Examples of region specifications are literally:
24-45, 56-78
1:45, 67=99;765..888
1,5,8,10,23,45,57,99

🌈 Additional section

  • -tolower toggle — this is how you "mask" a region by turning the sequence characters into lower-case. Some non-EMBOSS programs, e.g. fasta, will interpret that lowercase as a masked region. The sequence is unchanged apart from the case change, no cap 🧢. You might like to make sure the whole sequence is upper-case before you mask the specified regions to lower-case — do that with the '-supper' flag. Default value: N
  • -maskchar string — the character you use when masking. Default is 'X' for protein sequences and 'N' for nucleic sequences. If the mask character is set to the SPACE character or a null character, then the sequence gets "masked" by changing it to lower-case, just like with the '-lowercase' flag. Default value: @($(acdprotein)?X:N)

💜 Output section

  • -outseq seqout — where your freshly masked sequence goes. Slay.

😭 BUGS 😭

Found a bug? Not the vibe, but okay — 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). Be nice about it 💖

🔥 SEE ALSO 🔥

maskseq is fully documented via the tfm(1) system. iykyk.

🎀 AUTHOR 🎀

Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>

  • Wrote the script used to autogenerate this manual page. iconic behaviour, 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. periodt 💅

🌸 okay that's the whole page, no skips, no cuts, every single flag accounted for 🌸

and that's a wrap, bestie 🫶 this was EMBOSS 6.4.0, dated 05/11/2012, filed under MASKSEQ(1e) — go mask something iconic ✨🦋💜

📦 where this page comes from