GETSEQ(1)

✨ GETSEQ(1) ✨

okay bestie, so you know how we be yanking whole genomes out of databases?? this is the girl that does it. her name is getSeq and she prints genome sequences (or just lil slices of them) straight to standard output 💅

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🎀 NAME 🎀

getSeq — print genome sequences from databases on the standard output

🦋 SYNOPSIS 🦋

MySQL girlies:

getSeq [OPTIONS] --species=SPECIES --seq=SEQUENCE
--dbaccess=dbname,host,user,passwd

SQLite girlies:

getSeq [OPTIONS] --species=SPECIES --seq=SEQUENCE
--dbaccess=dbname.db --speciesfilenames=SPECIESFILENAMES

🌸 DESCRIPTION 🌸

Basically it grabs a genome sequence — or honestly just a part of one — from a MySQL database or a SQLite database. If you want, it'll hand you back the reverse complement instead. Either way, it prints to standard output. no cap, that's the whole vibe 🫶

💖 OPTIONS 💖

💫 Mandatory options (yes you actually need these, bestie)

• -s, --species=SPECIES — SPECIES is the species identifier you used when you loaded that sequence into the database. like, the name you gave it back then. you gotta match it fr.
• -q, --seq=SEQUENCE — SEQUENCE is the ID of the sequence you're trying to pull. this is your roman empire. go get her.
• -c, --dbaccess=database — the connection deets. and ok this one is different depending on your database situation:

MySQL: hand it a string with dbname, host, user, passwd all joined together with a comma. like a cute lil comma-separated polycule 🥰

• dbname — the name of the SQL database
• host — the host name or the IP
• user — the database user
• passwd — users and password

SQLite: it's just the file name of your SQLite database. ⚠️ and it must contain a dot — that's not optional, that's the rules.

• -f, --speciesfilenames=SPECIESFILENAMES — 👑 SQLite only, she does NOT know you otherwise, so don't even try it with MySQL. SPECIESFILENAMES is the file where the species identifier and the related file names of the sequences are stored. the format is:

Homo sapiens <TAB> /dir/to/genome/human.fa
Mus musculus <TAB> /dir/to/genome/mouse.fa

✨ Additional options (the little extras, the sprinkles)

• -a, --start=number — pull your subsequence starting at this position. and just so we're clear: coordinates are 1-based. do not come at her with 0. 🙈
• -b, --end=number — pull your subsequence ending at this position. also 1-based coordinates. consistency is the vibe.
• -r, --rc — outputs the reverse complement of the sequence. iconic behaviour honestly.
• -h, --help — produces the help message. when in doubt, ask her directly 💬

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🌈 EXAMPLE 🌈

MySQL, periodt:

getSeq --species=mouse --seq=chr16 --dbaccess=vertebrates,localhost,myuser,mypasswd
getSeq --species=human --seq=chr21 --start=32026 --end=32085 --rc --dbaccess=vertebrates,localhost,myuser,mypasswd

SQLite, same energy:

getSeq --species=mouse --seq=chr16 --dbaccess=vertebrates.db --speciesfilenames=speciesfilenames.tsv

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💜 AUTHORS 💜

AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth. absolute legends, we stan 🫡

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and that's the whole page bestie, GETSEQ(1) — brought to you by the AUGUSTUS girlies (that's M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth again, scream it 💖). now go pull some sequences, you ate. 🧚⭐