GENBANK_GET_...S_BY_TAXON.PY(1)

💖 genbank_get_genomes_by_taxon.py — the manual page, bestie edition 💖

okay so you're reading the man page for genbank_get_genomes_by_taxon.py, living in section 1 (User Commands), and honestly? it's giving "grab a whole bunch of genomes by their NCBI taxonomy ID." pull up a chair 🫶

✨ NAME ✨

genbank_get_genomes_by_taxon.py — genbank get genomes by taxon 🌸

✨ DESCRIPTION ✨

the vibe check, aka the usage line, is literally this:

usage: genbank_get_genomes_by_taxon.py [-h] -o OUTDIRNAME [-t TAXON]
[-v] [-f]

[--noclobber] [-l LOGFILE]
       [--format FORMAT] --email EMAIL [--retries RETRIES] [--batchsize
       BATCHSIZE] [--timeout TIMEOUT]

(no cap, that's exactly how it's spaced in the original. iconic formatting choices were made. we respect them 💅)

🌈 optional arguments 🌈

these are the little switches that make the magic happen, so let's go one by one, bestie:

• -h, --help — show this help message and exit. your classic "wait what does this do" button 🙈
• -o OUTDIRNAME, --outdir OUTDIRNAME — the output directory. and yes, it's required, so don't forget it or the program will simply not be having it 💀
• -t TAXON, --taxon TAXON — the NCBI taxonomy ID. that's your "which organism are we talking about" number 🦋
• -v, --verbose — give verbose output. more words! more updates! main character energy for your terminal ⭐
• -f, --force — force file overwriting. it will simply overwrite. bold of it, honestly 🔥
• --noclobber — don't nuke existing files. the polite option 🎀
• -l LOGFILE, --logfile LOGFILE — logfile location. so you know where the receipts live 🧾
• --format FORMAT — output file format, and your choices are [gbk|fasta] 🌸
• --email EMAIL — email associated with NCBI queries. required, because NCBI wants to know who's knocking 🫶
• --retries RETRIES — number of Entrez retry attempts per request. for when the network is being flaky 😭
• --batchsize BATCHSIZE — Entrez record return batch size. how many records come back at a time 📦
• --timeout TIMEOUT — timeout for URL connection, in seconds (s) ⏱️

lowkey important reminder: -o OUTDIRNAME / --outdir is required, and --email EMAIL is required. skip either one and you're not going anywhere, periodt. 💖

✨ AUTHOR ✨

this manpage was written by Nilesh Patra for the Debian distribution, and can be used for any other usage of the program. king behavior, truly 👑

and that's the whole thing!! this page is from July 2021, coming at you from genbank_get_genomes_by_taxon.py... — go get those genomes, bestie 💜🌈✨