LOAD2DB(1)

🎀 LOAD2DB — the load2db manual, but make it make sense 🎀

okay bestie, sit down, hydrate, and let me tell you about load2db(1) — she loads genome sequences AND extrinsic evidence hints straight into a MySQL database. iconic behavior honestly 💅

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✨ NAME ✨

load2db — loads genome sequences and extrinsic evidence hints into a MySQL database. that's her whole job, and she does it flawlessly no cap 🦋

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✨ SYNOPSIS ✨

load2db [OPTIONS] --species=SPECIES --dbaccess=dbname,host,user,passwd
inputfilename

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✨ DESCRIPTION ✨

so like. load2db is THE tool for loading genome sequences and extrinsic evidence hints into a MySQL database. 💖

⚠️ bestie please read this part twice: that database must be created before you call load2db. she does not create it for you. she will not hold your hand. create it first.

and when you're storing genomes/hints for multiple organisms? you just call this program over and over, once for each one. no multi-tasking, one organism at a time, we do it properly 🫶

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✨ OPTIONS ✨

inputfilename is either a genome file in FASTA format or a hints file in GFF format. pick your fighter 🌸

💖 Mandatory options 💖

these are non-negotiable, she's not asking, she's telling:

• -s, --species=SPECIES — SPECIES is a name for your species, and it's the same identifier you use in the treefile and alnfile parameters to augustus. yes, same one. consistency is the vibe check 🔥
• -d, --dbaccess=dbname,host,user,passwd — and inside that comma situation: dbname is the name of the SQL database, host is the host name or IP, user is the database user, and passwd is the password. four little values, one giant responsibility 👑

🌈 Additional options 🌈

• -c, --chunksize=size (⇐ 1000000) — ngl this one ONLY matters when you're loading a sequence file. what it does: your input genome gets split into chunks of this exact size, so that later, when something pulls a small sequence range, it doesn't have to read the entire — potentially way longer — chromosome. it's giving considerate ✨ Default Value: 50000
• -h, --help — produces the help message. when in doubt, ask her 💜

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✨ EXAMPLE ✨

first, create the database BEFORE calling load2db. mandatory. tutorial time:

create database before calling load2db:
 $ mysql -u root -p
 > CREATE DATABASE vertebrates;
 > CREATE USER 'myuser'@'%' IDENTIFIED BY 'mypasswd'; /* or whatever the password code is*/
 > GRANT ALL ON vertebrates.* TO 'myuser'@'%' IDENTIFIED BY 'mypasswd';

now look at her go 🏃♀️💨:

load2db --species=mouse --dbaccess=vertebrates,localhost,myuser,mypasswd mouse.fa
load2db --species=mouse --dbaccess=vertebrates,localhost,myuser,mypasswd mouse.hints.gff
load2db --species=human --dbaccess=vertebrates,localhost,myuser,mypasswd human.fa
load2db --species=human --dbaccess=vertebrates,localhost,myuser,mypasswd human.hints.gff

see the pattern? mouse.fa then mouse.hints.gff, human.fa then human.hints.gff. sequence file, then hints file. ate and left no crumbs 🍓

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✨ AUTHORS ✨

AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth. legends, truly, we thank them for their service 🙈💖

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and that's the whole load2db(1) situation, bestie 💫 you read the manual, you understood the manual, you're basically a database girlie now. go forth and load those genomes. periodt 💅🎀🦋