esl-seqrange(1)

📦
version 3.3.2 · 2 versions
, in fedora 43, fedora 44

💖 esl-seqrange — a whole manual, but make it bestie 💖

okay so this is the manual page for esl-seqrange, part of the Easel manual. if you're splitting a big sequence file across a bunch of parallel processes and you need to know which chunk is mine, bestie, this is literally the tool. 🦋

✨ NAME ✨

esl-seqrange — figure out which range of sequences belongs to one of a whole bunch of parallel processes 💅

✨ SYNOPSIS ✨

esl-sfetch [options] seqfile procidx nproc

(no that's not a typo, that's literally what the page says, we keep it exactly as-is 🫶)

✨ DESCRIPTION ✨

okay so picture this: you've got an SSI-indexed seqfile, and you've got nproc total processes all tryna chew through it at the same time. esl-seqrange reads that file and tells you the range of sequence indices that process number procidx — out of nproc total processes — should be operating on. that's it. that's the whole job. and it ate. 👑

⚠️ real talk: the seqfile must be indexed first, using esl-sfetch --index seqfile. that creates an SSI index file called seqfile.ssi. an SSI file is required for esl-seqrange to work at all — no index, no vibe. 💀

so how does it split things up? the rule is simple, lowkey elegant: every process should get the same number of sequences, or as close to the same as physically possible. equal-ish slices for everyone. 🍓

and here's the thing — it does not look at the lengths of the sequences. like, not even a little. which, ngl, it probably should?? the manpage itself says so ("even though they probably should be"). iconic self-aware king behavior honestly. 🙈

✨ OPTIONS ✨

  • -h — prints a brief lil help message, and yeah it throws in the version number plus a summary of all the options, expert ones included. the whole menu. 🌸
  • --informat <s> — asserts that the input seqfile is in format <s>, which skips the whole format-autodetection thing. common choices for <s> include: fasta, embl, genbank. alignment formats also work!! common ones include: stockholm, a2m, afa, psiblast, clustal, phylip. for more info, and for the codes for some of the less common formats, go check the main documentation. also the string <s> is case-insensitive, so fasta or FASTA both work — she does not care about your capitalization choices. 💅

✨ SEE ALSO ✨

Copyright (C) 2020 Howard Hughes Medical Institute. Freely distributed under the BSD open source license. (open source!! we love to see it 💖)

✨ AUTHOR ✨

http://eddylab.org

and that's the whole page, bestie — this was Easel version 0.48, dated Nov 2020, and the manual page is esl-seqrange(1) from the Easel Manual. go forth and parallelize responsibly 🧚✨💜

📦 where this page comes from