COMPSEQ(1e)

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

💖 compseq(1e) — the composition girlie 💖

okay bestie, so this is a page from the EMBOSS manual (that's "the European Molecular Biology Open Software Suite", yes the whole thing, iconic name, no notes) and it lives in the Debian packaging of it. compseq is a command line program, and it's part of the "Nucleic:Composition,Protein:Composition" command group(s). Basically: it counts up the composition of unique words in sequences. slay. 💅

✨ NAME ✨

compseq — Calculate the composition of unique words in sequences 🧬

✨ SYNOPSIS ✨

compseq -sequence seqall [-infile infile] -word integer [-frame integer]
        -ignorebz boolean -reverse boolean [-calcfreq boolean]
        -outfile outfile [-zerocount boolean]

compseq -help

✨ DESCRIPTION ✨

compseq is a command line program from EMBOSS ("the European Molecular Biology Open Software Suite"). It's part of the "Nucleic:Composition,Protein:Composition" command group(s). 🫶

✨ OPTIONS ✨

🌸 Input section 🌸

  • -sequence seqall — your sequence input, bestie. this is the seqall you're feeding in. 🌈
  • -infile infile — this is a file that was previously produced by compseq, and you can use it to set the expected frequencies of words in this analysis. lowkey important: the word size in the current run has to be the same as the one in this results file, fr fr. and obviously (obviously!!) you should use a file produced from protein sequences if you're counting protein sequence word frequencies, and you must use one made from nucleotide frequencies if you're analysing a nucleotide sequence. no mixing, we don't do that here. 🙈

🌟 Required section 🌟

  • -word integer — this is the size of word (n-mer) to count. so if you wanna count codon frequencies for a nucleotide sequence, you'd enter 3 here. it's giving "how big is my word". default value: 2 ✨

💫 Additional section 💫

  • -frame integer — the normal behaviour of compseq is to count the frequencies of all words that occur by moving a window of length word up by one each time. this option lets you move the window up by the length of the word each time instead, skipping over the intervening words. you can count only those words that occur in a single frame of the word by setting this value to a number other than zero. set it to 1 and it'll only count the words in frame 1, 2 will only count the words in frame 2, and so on. main character window-shifting energy. 🦋
  • -ignorebz boolean — the amino acid code B represents Asparagine or Aspartic acid, and the code Z represents Glutamine or Glutamic acid. these are not commonly used codes, and you may wish not to count words containing them — just noting them in the count of 'Other' words instead. default value: Y 🎀
  • -reverse boolean — set this to be true if you also wish to also count words in the reverse complement of a nucleic sequence. default value: N 🔄
  • -calcfreq boolean — if this is set true then the expected frequencies of words are calculated from the observed frequency of single bases or residues in the sequences. if you're reporting a word size of 1 (single bases or residues) then there is no point in using this option, because the calculated expected frequency will be equal to the observed frequency — like, why would you. calculating the expected frequencies like this will give an approximation of the expected frequencies that you might get by using an input file of frequencies produced by a previous run of this program. and heads up: if an input file of expected word frequencies has been specified, then the values from that file will be used instead of this calculation of expected frequency from the sequence, even if 'calcfreq' is set to be true. default value: N 🧚

👑 Output section 👑

  • -outfile outfile — this is the results file. that's it, that's the vibe. 💖
  • -zerocount boolean — you can make the output results file much smaller if you do not display the words with a zero count. default value: Y ⭐

💀 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). tell them everything, bestie. 😭

🌈 SEE ALSO 🌈

compseq 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. (ty for your service 🫡)

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. 📜

ok that's the whole page, no skips, no crumbs left behind. periodt. 💅✨

and finally, the cute little sign-off: this was EMBOSS 6.4.0, dated 05/11/2012, and yes it is the COMPSEQ(1e) page. bye bestie, go count some words 🎀🦋💖

📦 where this page comes from