sindex(1)

💖 NAME 💖

okay so first things first, this whole thing lives in the Biosquid Manual, and the star of the show is sindex — she indexes a sequence database for sfetch so your future self can retrieve sequences without any drama ✨

🦋 SYNOPSIS 🦋

sindex [options] seqfile1 [seqfile2...]

🌸 DESCRIPTION 🌸

so bestie, here's the tea: sindex indexes one or more seqfiles so that sfetch can come back later and grab sequences out of them. It builds an SSI file — that's a "squid sequence index" — and drops it in the same directory as the sequence files. By default it's literally just called <seqfile>.ssi, no cap 💅

now here's the part where you gotta pay attention 👀 if you put more than one sequence file on the command line, the SSI filename gets constructed from the last sequence file name. And that might not be the vibe you were going for, fr fr. So if you want a different name, go look at the -o option and name your own SSI file, periodt.

also!! sindex is capable of indexing large files (>2 GB) if optional LFS support got enabled at compile-time. like, it's giving big-file energy but only when that build flag said yes. check the INSTALL instructions that came with @PACKAGE@ for the deets 📦

✨ OPTIONS ✨

• -h — prints a lil brief help situation; it's got the version number and a summary of all the options, expert options included 🫶
• -o <ssi outfile> — sends the SSI index to a file named <outfile> instead of wherever it would've gone. By default the SSI file would've gone to <seqfile>.ssi, so this is your moment to take the wheel 🎀

🔥 EXPERT OPTIONS 🔥

these are the advanced ones, iykyk — handle with care, bestie 😭

• --64 — forces the SSI file into 64-bit (large seqfile) mode, even if the seqfile is tiny. and like… you genuinely do not want to do this unless you're debugging. not me warning you twice 💀
• --external — forces sindex to do its record sorting by external (on-disk) sorting. also only useful for debugging, same energy as above, no cap.
• --informat <s> — declares that the sequence file is definitely in format <s>, which blocks sequence file format autodetection. super useful in automated pipelines because it improves robustness (autodetection can occasionally go wrong on a perversely malformed file, and that's the villain origin story fr). common examples include genbank, embl, gcg, pir, stockholm, clustal, msf, or phylip; see the printed documentation for the complete list of accepted format names 📚
• --pfamseq — a hack for Pfam 🧚 it indexes a FASTA file that's known to have identifier lines in the format >[name] [accession] [optional description]. normally only the sequence name would get indexed as a primary key in a FASTA SSI file, but this lets you index both the name (as a primary key) and the accession (as a secondary key). iconic behavior honestly 👑

🌈 SEE ALSO 🌈

afetch(1), alistat(1), compalign(1), compstruct(1), revcomp(1), seqsplit(1), seqstat(1), sfetch(1), shuffle(1), sreformat(1), stranslate(1), weight(1). go read the whole squad, they all ate 💖

👑 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, mwah 💋 this lil manual shipped with Biosquid 1.9g back in January 2003 — old but gold, and yes she's still serving 💅✨