NCBI_SEARCH(1)

🌸 ncbi_search(1) — a user command, bestie 💖

okay so real talk: this is the ncbi_search manual page, and it lives in section 1 of the manual (that's the "user commands" girlies, iykyk). she's cute, she's useful, and she is lowkey iconic for anyone comparing bacterial, plasmid, chloroplast, or mitochondrial sequences. let's get into it ✨

✨ NAME ✨

ncbi_search — for visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences 🦠🧬

🌈 DESCRIPTION 🌈

💅 USAGE:

ncbi_search -q STRING -o FILE -d STRING -r STRING [Options]

🫶 DESCRIPTION:

she uses NCBI's eSearch to download collections of sequences. that's the whole vibe. no cap.

👑 REQUIRED ARGUMENTS:

yes bestie, these are required. she is not doing it without them. periodt.

• -q, --query [STRING] — the raw query text, exactly how you'd type it. just the actual words of your search, no makeup on it.
• -o, --output [FILE] — the output file she should create. BUT — if you also pass the split option, this should be a directory, and the returned records get written in there instead. and if that directory doesn't exist yet? she'll just make it. she's proactive like that 💅
• -d, --database [STRING] — the name of the NCBI database to search. think like 'nucleotide', 'protein', or 'gene'.
• -r, --return_type [STRING] — the type of info you're requesting. for sequences, 'fasta' is the one people reach for a lot. ngl the accepted formats vary depending on which database you're querying, so check what your database actually supports.
• -s, --split — return each record as its own separate file, and the filename will be the accesssion id of the record. ⚠️ this one only works if the return_type is 'gb' or 'gbwithparts'. no gb, no split, sorry babe.
• -m, --max_records [INTEGER] — the max number of records to return. the default is to return all the matches satisfying the query, so like... go off, but that could be a lot 🍓
• -v, --verbose — provide progress messages. she'll talk you through it, main character energy fr fr.
• -h, --help — show this message. the classic.

🎀 EXAMPLE:

ncbi_search -q 'dysphagia AND homo sapiens[ORGN]' \
-o results.txt -d pubmed -r uilist -m 100

💜 AUTHOR 💜

this manpage was written by Andreas Tille</purl> for the Debian distribution, and can be used for any other usage of the program. king behavior honestly 👑

okay that's the whole page bestie, go download some sequences 💖

this was ncbi_search version 20170919, dated August 2018 — love that for her, vintage era 🦋✨