KTGETTAXINFO(1)

💖 ktGetTaxInfo — the vibe check on your metagenomic data 💖

okay so bestie, welcome to ktGetTaxInfo from the User Commands crew ✨ this little icon literally helps you explore hierarchical metagenomic data with zoomable pie charts 🥧🌈 no cap, it's giving main character energy for your taxonomy lookups.

🌸 NAME 🌸

ktGetTaxInfo — explore hierarchical metagenomic data with zoomable pie charts 🦋

✨ DESCRIPTION ✨

so here's the tea, bestie 🫖:

It retrieves taxonomy information for accessions or taxonomy IDs. You can hand those over as arguments, or it'll grab them from the first field of <stdin> — and yeah, they're separated by whitespace, just fyi 💅

Now, the important part: if the input is a number, it is assumed to be a taxonomy ID. If it's not a number, it gets treated as an accession or a sequence ID that has an accession hiding in the fourth field of pipe notation 👀 like this:

gi|12345|xx|ABC123.1|

and yes, it ignores fasta/fastq tag markers [>,@] — so no stress about those little symbols, they're not gonna trip anything up 🎀

🫶 Now the sad part: if taxonomy information was not found for a given input line, the output line will be only the taxonomy ID, which will be 0 if it was looked up from an accession but not found. Not the slay we wanted but at least you know what happened 😭

The output fields, in order, are:

taxID  depth  parent  rank  name

periodt. 💅

🧚 Usage

ktGetTaxInfo [IDs ...] [< ID_list] > tax_info

🌈 Command line example

ktGetTaxInfo A00001.1 "gi|2|emb|A00002.1|" 9606

🍓 Fasta tag example

grep ">" sequence.fasta | ktGetTaxInfo

look at that pipeline glow-up 🔥

👑 OPTIONS 👑

• -p — Prepend tax info to the original lines (separated by tabs). putting the new stuff first, as a treat ✨
• -a — Append tax info to the original lines (separated by tabs). new stuff goes at the end, ngl very demure 🎀
• -f <integer> — Field of accessions. [Default: '1'] — tell it which field your accessions are living in, bestie 💅
• -tax <string> — Path to directory containing a taxonomy database to use. point it at your tax db and let it cook 🍳

and that's the whole thing, bestie!! 🦋 go forth and get those tax IDs 💖

this page is for ktGetTaxInfo 2.8, dated June 2021 🎀 ily, go slay your metagenomics ✨💅👑