esl-sfetch(1)

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

💅 esl-sfetch — straight from the Easel manual, bestie 💅

okay so. this is the manual page for esl-sfetch, coming at you from the Easel manual set. it is iconic, it is useful, and by the end of this you will be fetching sequences like the main character you are. no cap. 🦋

✨ NAME ✨

esl-sfetch — grab (sub-)sequences out of a sequence file, like a lil' sequence vending machine 🌸

✨ SYNOPSIS ✨

esl-sfetch [options] seqfile key
  (retrieve a single sequence by key)

esl-sfetch -c from..to [options] seqfile key
  (retrieve a single subsequence by key and coords)

esl-sfetch -f [options] seqfile keyfile
  (retrieve multiple sequences using a file of keys)

esl-sfetch -Cf [options] seqfile subseq-coord-file
  (retrieve multiple subsequences using file of keys and coords)

esl-sfetch --index msafile
  (index a sequence file for retrievals)

✨ DESCRIPTION ✨

so esl-sfetch pulls one or more sequences, or subsequences, out of seqfile. that's the whole vibe. 💖

but first — the tea ☕ — your seqfile must be indexed first, using esl-sfetch --index seqfile. that makes an SSI index file called seqfile.ssi. do it once, thank yourself forever.

wanna grab one whole sequence? just do esl-sfetch seqfile key, where key is the name or the accession of the sequence you're obsessed with. simple as.

wanna grab one subsequence instead of the whole thing? use the -c start..end option and hand over start and end coordinates. those two coords go in as one single string, separated by any nonnumeric, nonwhitespace character (or characters!) you feel like — pick your fave separator, it's your world. more deets down in the -c option below 👇

wanna grab more than one complete sequence at once? that's the -f option, and now the second command line argument is the name of a keyfile — a file holding a list of names or accessions, one per line. the first whitespace-delimited field on each line is what gets parsed as the name/accession. periodt.

wanna grab more than one subsequence at once? add -C on top of -f, and now that second argument gets parsed as a list of subsequence coordinate lines instead. the format of those lines lives down in the -C option below — go peek 👀

now for the DNA/RNA girlies 🧬 — you can extract (sub-)sequences in reverse complement orientation in two different ways: either hand over a from coordinate that's greater than to, or just use the -r option. two paths, same slay.

and when you're using -f for multiple (sub-)sequence retrieval, the file argument can be - (a single dash), and then the list of names/accessions (or subsequence coordinate lines) gets read from standard input instead. cute! BUT — and this is the important part, bestie — a standard input stream can't be SSI indexed, so (sub-)sequence retrieval from stdin may be slow. i'm just saying. 🙈

✨ OPTIONS ✨

  • -h — print a brief help message, and yeah it throws in the version number plus a summary of all the options, even the expert ones. a little snack. 🍓
  • -c coords — retrieve a subsequence, with start and end coordinates given by the coords string. that string is just start and end coords separated by any nonnumeric, nonwhitespace character or characters you like; for example, -c 23..100, -c 23/100, or -c 23-100 all work. want a suffix of a subsequence? you can straight up omit the end; for example, -c 23: works. and to specify reverse complement (for DNA/RNA sequence), you can specify from greater than to; for example, -c 100..23 retrieves the reverse complement strand from 100 to 23. ✨
  • -f — interpret the second argument as a keyfile instead of just one key. the first whitespace-limited field on each line of keyfile is interpreted as a name or accession to be fetched. ⚠️ this option doesn't work with the --index option. any other fields on a line after the first one are ignored. blank lines and lines beginning with # are ignored. so you can comment your keyfiles, bestie, live your truth.
  • -o <f> — output the retrieved sequences to a file <f> instead of to stdout.
  • -n <s> — rename the retrieved (sub-)sequence <s>. 🚫 incompatible with -f.
  • -r — reverse complement the retrieved (sub-)sequence. only accepted for DNA/RNA sequences. 🧬
  • -C — multiple subsequence retrieval mode, with the -f option (required). this says the second command line argument is to be parsed as a subsequence coordinate file, made of lines containing four whitespace-delimited fields: new_name, from, to, name/accession. for each such line, the sequence name/accession is found, a subsequence from..to is extracted, and that subsequence gets renamed to new_name before it's output. any other fields after the first four are ignored. blank lines and lines beginning with # are ignored. 💅
  • -O — output the retrieved sequence to a file named key. this is a convenience so you save some typing: instead of
% esl-sfetch -o SRPA_HUMAN swissprot SRPA_HUMAN

you can just type

% esl-sfetch -O swissprot SRPA_HUMAN

the -O option only works if you're retrieving a single alignment; it is incompatible with -f.

  • --index — instead of retrieving a key, the special command esl-sfetch --index seqfile produces an SSI index of the names and accessions of the alignments in the seqfile. indexing should be done once on the seqfile to prepare it for all future fetches. do it once, fetch forever. 👑

✨ EXPERT OPTIONS ✨

these are for when you're feeling fancy, bestie. 😌

  • --informat <s> — assert that seqfile is in format <s>, bypassing format autodetection. common choices for <s> include: fasta, embl, genbank. alignment formats also work; common choices include: stockholm, a2m, afa, psiblast, clustal, phylip. for more information, and for codes for some less common formats, see the main documentation. the string <s> is case-insensitive (fasta or FASTA both work). 🌈

✨ SEE ALSO ✨

Copyright (C) 2020 Howard Hughes Medical Institute.

Freely distributed under the BSD open source license.

✨ AUTHOR ✨

http://eddylab.org

and that's the whole page, bestie 🫶 this was Easel 0.48, from Nov 2020 — go forth and fetch, you absolute legend. 💜✨

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