sfetch(1)

💅 sfetch(1) — the Biosquid Manual, but make it a group chat

okay bestie, buckle up, because this is sfetch from the Biosquid Manual and it is literally the little tool that goes and gets your sequence for you. one sequence, one name, boom. let's get into it 🫶

✨ NAME ✨

sfetch — get a sequence from a flatfile database. that's it. that's the whole job. and it eats every single time 👑

🌸 SYNOPSIS 🌸

sfetch [options] seqname

🦋 DESCRIPTION 🦋

so sfetch goes and retrieves the sequence named seqname out of a sequence database. iconic behaviour, no notes.

which database it hits is decided by the -d and -D options — or, as the cool kids say, "little databases" and "big databases". the directory location of the "big databases" can be given to you via environment variables, like $SWDIR for Swissprot and $GBDIR for Genbank (peep -D for the complete list, don't be shy). for "little databases" you have to spell out a complete file path, every time, no shortcuts. and by default? if neither option is specified and the name looks like a Swissprot identifier (like, it has a _ character in it, iykyk), then the $SWDIR environment variable gets used to attempt to retrieve the sequence seqname from Swissprot. the vibes decide. 💅

there are a whole bunch of other options too, and they are giving range: retrieval of subsequences (-f, -t); retrieval by accession number instead of by name (-a); reformatting the extracted sequence into a variety of other formats (-F); etc. so much etc. we love a versatile queen.

okay now the important part, bestie. if the database has been SSI indexed, sequence retrieval will be extremely efficient. but if it has NOT been indexed? retrieval may be painfully slow — like, the entire database may have to be read into memory just to find seqname. the whole thing. into memory. to find one sequence. 😭 so yeah, SSI indexing is recommended for all large or permanent databases. the program sindex creates SSI indexes for any sequence file. go index your stuff, fr fr.

also fun lore: sfetch was originally named getseq, and it got renamed because it clashed with a GCG program of the same name. messy. but we move. 💖

🎀 OPTIONS 🎀

• -a — interpret seqname as an accession number, not an identifier. different kind of lookup, same slay.
• -d <seqfile> — retrieve the sequence from a sequence file named <seqfile>. and listen, if a GSI index <seqfile>.gsi exists, it gets used to speed up the retrieval. glow up courtesy of indexing ✨
• -f <from> — extract a subsequence starting from position <from>, rather than from 1. see -t for the other half of this situationship. but heads up: if <from> is greater than <to> (as specified by the -t option), then the sequence is extracted as its reverse complement (it is assumed to be nucleic acid sequence). plot twist 🌀
• -h — print brief help; includes version number and summary of all options, including expert options. the "just tell me everything" button. very demure, very mindful.
• -o <outfile> — direct the output to a file named <outfile>. by default, output would go to stdout. but you can absolutely make it go somewhere fancy instead.
• -r <newname> — rename the sequence <newname> in the output after extraction. by default, the original sequence identifier would be retained. useful, for instance, if retrieving a sequence fragment; the coordinates of the fragment might be added to the name (this is what Pfam does). main character rename energy 👑
• -t <to> — extract a subsequence that ends at position <to>, rather than at the end of the sequence. see -f. and again, plot twist: if <to> is less than <from> (as specified by the -f option), then the sequence is extracted as its reverse complement (it is assumed to be nucleic acid sequence). no closing period in the original on this one, so we're keeping the chaos. 🙈
• -D <database> — retrieve the sequence from the main sequence database coded <database>. for each code, there is an environment variable that specifies the directory path to that database. the recognized codes and their corresponding environment variables are: -Dsw (Swissprot, $SWDIR); -Dpir (PIR, $PIRDIR); -Dem (EMBL, $EMBLDIR); -Dgb (Genbank, $GBDIR); -Dwp (Wormpep, $WORMDIR); and -Dowl (OWL, $OWLDIR). each database is read in its native flatfile format. six whole databases, six whole vibes 🌈
• -F <format> — reformat the extracted sequence into a different format. (by default, the sequence is extracted from the database in the same format as the database.) the available formats are embl, fasta, genbank, gcg, strider, zuker, ig, pir, squid, and raw. ten formats. a whole wardrobe. 💅

💜 EXPERT OPTIONS 💜

• --informat <s> — specify that the sequence file is in format <s>, rather than the default FASTA format. common examples include Genbank, EMBL, GCG, PIR, Stockholm, Clustal, MSF, or PHYLIP; see the printed documentation for a complete list of accepted format names. and this one is highkey powerful because it overrides the default format (FASTA) and the -B Babelfish autodetection option. no takebacks. ⭐

🔥 SEE ALSO 🔥

afetch(1), alistat(1), compalign(1), compstruct(1), revcomp(1), seqsplit(1), seqstat(1), shuffle(1), sindex(1), sreformat(1), stranslate(1), weight(1). the whole friend group. go say hi. 🫶

👑 AUTHOR 👑

Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine. Freely distributed under the GNU General Public License (GPL). See COPYING in the source code distribution for more details, or contact me.

Sean Eddy HHMI/Department of Genetics Washington University School of Medicine 4444 Forest Park Blvd., Box 8510 St Louis, MO 63108 USA Phone: 1-314-362-7666 FAX : 1-314-362-2157 Email: eddy@genetics.wustl.edu

and that's the whole page, bestie!! this was Biosquid 1.9g, dated January 2003 — yeah, she's an elder icon but she still runs the game. periodt. 💖✨🎀🦋