LOAD2SQLITEDB(1)

💖 load2sqlitedb — the manual, but make it cute 💖

okay bestie, welcome to the LOAD2SQLITEDB(1) glow-up ✨ this is the AUGUSTUS tool that yeets your genome sequences and extrinsic evidence hints straight into a SQLite database. buckle up 🎀

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🌸 NAME 🌸

load2sqlitedb — loads genome sequences and extrinsic evidence hints into a SQLite database 🦋

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✨ SYNOPSIS ✨

load2sqlitedb [OPTIONS] --species=SPECIES --dbaccess=database.db
inputfilename

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💅 DESCRIPTION 💅

so like, load2sqlitedb is the tool that loads genome sequences and extrinsic evidence hints into a SQLite database. that's the whole vibe. 💾

and the way that you've got multiple organisms?? you literally just call this program again and again, once for each one. no cap. 🔁

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👑 OPTIONS 👑

inputfilename is either a genome file in FASTA format or a hints file in GFF format. yes bestie, the file type decides what it does. 🌈

🎀 Mandatory options (not optional, i fear)

• -s, --species=SPECIES — SPECIES is a name for your species, and it's gotta be the same identifier as what you use in the treefile and alnfile parameters for augustus. consistency is the moment. 🫶
• -d, --dbaccess=database.db — the file name of the SQLite database. it gets opened, or created if it doesn't already exist. iconic behaviour honestly. ✨

🦋 Additional options

• -c, --chunksize=size — this one is only relevant when you're loading a sequence file. the sequences in the input genome get split into chunks of this size, so that later retrievals of small sequence ranges don't have to read the complete chromosome — which could be, like, way way longer. (⇐ 1000000). Default Value: 50000 🍓
• -i, --noIdx — use this flag to suppress building of indices on the database tables. if you're gonna load several genomes and/or hint files one after another, this is recommended because it speeds up the loading. BUT bestie, make sure you build the indices with --makeIdx after all genomes/hints are loaded. otherwise data retrieval operations can be very slow. consider this your vibe check 🚨
• -m, --makeIdx — use this flag to build the indices on the database tables after loading several genomes and/or hint files with --noIdx. only call it once for all species, e.g. load2sqlitedb --makeIdx --dbaccess=database.db 👑
• -r, --clean — makes a clean load, deleting existing hints/genome for the species from the database. ⚠️ when called with a gff file, only the hints for the species are deleted, not the genome. when called with a fasta file, both hints and genome for the species are deleted. so like... know which one you're feeding it 💀
• -h, --help — produce help message. the classic. 🙈

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🌟 EXAMPLE 🌟

load2sqlitedb --species=mouse --dbaccess=vertebrates.db mouse.fa
load2sqlitedb --species=mouse --dbaccess=vertebrates.db mouse.hints.gff
load2sqlitedb --species=human --dbaccess=vertebrates.db human.fa
load2sqlitedb --species=human --dbaccess=vertebrates.db human.hints.gff

look at that. mouse first, then human. vertebrates only. slay. 🔥

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💜 AUTHORS 💜

AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth. absolute legends, fr fr 🙌

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and that's the whole page bestie 💖 this one signs off as LOAD2SQLITEDB(1), straight out of the AUGUSTUS manual set — no fancy date stamp on it, just the name, and honestly? it ate. go forth and load your genomes 🧚✨

periodt. 💅