esl-afetch(1)

💖 esl-afetch — the Easel manual page, bestie edition 💖

okay so you found the esl-afetch(1) page in the Easel Manual and you're like "what is this" — don't worry, I gotchu. this is your alignment-fetching bestie and she is so good at her job. 🦋

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✨ NAME ✨

esl-afetch — retrieve alignments from a multi-MSA database 👑

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🌸 SYNOPSIS 🌸

single MSA retrieval, the classic:

esl-afetch [options] msafile key

multiple MSA retrieval, when you're pulling a whole file of keys:

esl-afetch -f [options] msafile keyfile

and the indexing era:

esl-afetch --index msafile

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💅 DESCRIPTION 💅

so esl-afetch goes and gets the alignment named key out of an alignment database living in the file msafile. simple as that, no cap.

the msafile is a "multiple multiple alignment" file in Stockholm format (think native Pfam or Rfam — you know the vibe). and the key? it's either the name (the ID) of the alignment, or its accession number (AC). either one works, she's flexible like that. 💖

now, alternatively, esl-afetch -f gives you the ability to fetch a whole bunch of alignments at once. the -f option makes it interpret that second argument as a keyfile — literally a file consisting of one name or accession per line. one per line. that's it. that's the whole format. iconic. ✨

💀 heads up: the msafile should first be SSI indexed with esl-afetch --index for efficient retrieval. an SSI index is not required, but without one, alignment retrieval may be painfully slow. and I mean painfully. like waiting for your phone to load a 2014 tumblr blog painfully. 😭

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🎀 OPTIONS 🎀

• -h — print brief help; includes the version number and a summary of all options, including the expert options. the "hi bestie, what do I do" flag. 🙈
• -f — interpret the second argument as a keyfile instead of as just one key. the keyfile contains one name or accession per line. this option does not work with the --index option. ✋
• -o <f> — output retrieved alignments to a file <f> instead of to stdout. send it somewhere nice. 🫶
• -O — output retrieved alignment to a file named key. it's a convenience for saving some typing, and honestly? we love efficiency. instead of:

% esl-afetch -o RRM_1 msafile RRM_1

you can just type:

% esl-afetch -O msafile RRM_1

the -O option only works if you're retrieving a single alignment; it is incompatible with -f. one at a time, queen. 👑

• --index — instead of retrieving a key, the special command esl-afetch --index msafile produces an SSI index of the names and accessions of the alignments in the msafile. indexing should be done once on the msafile to prepare it for all future fetches. do it once, thank yourself forever. that's main character energy fr fr. 🔥

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🌈 SEE ALSO 🌈

• http://bioeasel.org/

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💜 COPYRIGHT 💜

Copyright (C) 2020 Howard Hughes Medical Institute.

Freely distributed under the BSD open source license. (slay, open source.) 🌸

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🧚 AUTHOR 🧚

• http://eddylab.org

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and that's the whole page, bestie!! go forth and fetch those alignments. ✨🦋💖

Easel 0.48 — Nov 2020 — mwah, take care of her 💅🎀