SEQFRAGGLE(1e)

📦 version 0.1.660, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

✨ SEQFRAGGLE 💅

okay bestie, so this is seqfraggle(1e) — like, the page is from the EMBOSS Manual for Debian and it's literally about yeeting fragment sequences out of DHF files 🦋

🌸 NAME 🌸

seqfraggle — removes fragment sequences from DHF files. that's it. that's the whole job. iconic behaviour honestly 🎀

✨ SYNOPSIS ✨

seqfraggle -dhfinpath dirlist -thresh integer -dhfoutdir outdir

seqfraggle -help

💖 DESCRIPTION 💖

seqfraggle is a command line program from EMBOSS (the European Molecular Biology Open Software Suite — say that five times fast, I dare you 😭). It belongs to the "Protein:3D Structure" command group(s), so it's out here running with the structure girlies 👑

🫶 OPTIONS 🫶

🌈 Input section

  • -dhfinpath dirlist — this one tells it where your DHF files (domain hits files) live, or honestly any other sequence files you're feeding in as input. A 'domain hits file' contains database hits (sequences) with domain classification information, in FASTA or EMBL formats. Those hits are relatives to a SCOP or CATH family and they're found from a search of a sequence database. Files containing hits retrieved by PSIBLAST get generated by using SEQSEARCH. Or, plot twist, SEQFRAGGLE will also accept sequence or sequence sets in any of the common formats. Default value: ./

🔥 Required section

  • -thresh integer — this is the percentage of median length that defines what counts as a fragment, no cap. Here's the tea: SEQFRAGGLE first figures out the median length of all the sequences in the input file, then discards any hit sequences that are not within a threshold percentage of that median length. Whatever survives gets written to the output file. Default value: 50

🎀 Output section

  • -dhfoutdir outdir — where the DHF files (domain hits files) get written (output). A 'domain hits file' contains database hits (sequences) with domain classification information, in FASTA or EMBL formats. The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH. Alternatively, SEQFRAGGLE will write output files in any of the common formats. Default value: ./

💀 BUGS 💀

Found a bug? bestie, report it 🙈 you've got options:

⭐ SEE ALSO ⭐

seqfraggle 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. (yes, a script wrote this. we're all just out here living our main character lives I guess 😭💅)

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.

k that's the whole page bestie, go frag some sequences responsibly 💖✨

this lil beauty came from the DOMSEARCH package, version 0.1.0++20100721, dated 08/11/2010 — shoutout to the EMBOSS girlies for the whole vibe 🦋

📦 where this page comes from