KTIMPORTFCP(1)

💖 ktImportFCP — the manual, but make it cute 💖

okay bestie, this is ktImportFCP(1), a User Commands page, and it's genuinely iconic. sit down, grab a boba, we're exploring hierarchical metagenomic data with zoomable pie charts 🥧✨

✨ NAME ✨

ktImportFCP — explore hierarchical metagenomic data with zoomable pie charts 🦋

🌸 DESCRIPTION 🌸

It makes a Krona chart out of the results of FCP (the Fragment Classification Package). that's the whole vibe. no cap.

ktImportFCP \
    [options] \
    fcp_output_1[:magnitudes_1][,name_1] \
    [fcp_output_2[:magnitudes_2][,name_2]] \
    ...

here's what all those lil pieces mean, one by one 🫶

• fcp_output — this is the output you get from running any FCP classification tool. heads up though: BLASTN.py is the exception, because it only outputs raw BLAST results. by default you get separate datasets for each input file (unless you pass [-c], more on her below 👇).
• magnitudes — an optional file that lists query IDs alongside magnitudes, separated by tabs. this is the glow-up that lets you account for read length or contig depth so your abundance numbers are actually accurate. by default, any query sequences with no specified magnitudes get a magnitude of 1. and if you've got assemblies in ACE format, you can make magnitude files with ktGetContigMagnitudes 💅
• name — a name to show in the list of datasets inside the Krona chart. this one matters when multiple input files are present and [-c] is not specified. by default it just uses the basename of the file. lowkey sensible.

🎀 the options 🎀

• [-o <string>] — output file name. [Default: 'fcp.krona.html']
• [-n <string>] — name of the highest level. [Default: 'root']
• [-c] — combine data from each file instead of creating separate datasets within the chart. bestie behavior fr fr.
• [-d <integer>] — maximum depth of wedges to include in the chart. that's it, that's the whole option.
• [-u <string>] — URL of Krona resources to use instead of bundling them with the chart (e.g. "http://krona.sourceforge.net"). it reduces the size of your charts and allows updates, though charts will not work without access to this URL ⚠️ so like… know what you're doing.
• [-qp <string>] — url to send query IDs to (instead of listing them) for each wedge. the query IDs get sent as a comma separated list in the POST variable "queries", with the current dataset index (from 0) in the POST variable "dataset". the url can include additional variables encoded via GET. she's fancy, she's doing the most, we respect it 💜

no cap: every flag above is doing exactly what it says and nothing more, so don't go inventing extra behavior for her 🙈

that's the page, bestie. this was ktImportFCP 2.8, dated June 2021, and it's giving main character energy all the way through 🌈👑 mwah, slay, periodt 💅💖