KTIMPORTTAXONOMY(1)

✨ NAME ✨

okay so bestie, meet ktImportTaxonomy — it's the manual page (section 1, user commands 💅) for the tool that lets you explore hierarchical metagenomic data with zoomable pie charts. 🥧🦋 iconic behavior honestly.

🌸 DESCRIPTION 🌸

so what it does: it creates a Krona chart based on taxonomy IDs and, optionally, magnitudes and scores. 🎀

and here's the lil glow-up it does for you: taxonomy IDs that correspond to a rank of "no rank" in the database get assigned to their parents so the hierarchy stays less cluttered. like for example, "Cellular organisms" will be assigned to "root". it's giving tidy. ✨

here's the whole vibe, the shape of the command:

ktImportTaxonomy \

[options] \ taxonomy_1[:magnitudes_1][,name_1] \
[taxonomy_2[:magnitudes_2][,name_2]] \ ...

🫶 the inputs, explained

• taxonomy — a tab-delimited file with taxonomy IDs and (optionally) query IDs, magnitudes and scores. by default, query IDs, taxonomy IDs and scores will be taken from columns 1, 2 and 3, respectively (peep -q, -t, -s, and -m for that). lines beginning with "#" will be ignored, no cap. and by default, separate datasets will be created for each input (see [-c]).
• magnitudes — an optional file listing query IDs with magnitudes, separated by tabs. this one is lowkey important: it can be used to account for read length or contig depth to obtain a more accurate representation of abundance. 📈 by default, query sequences without specified magnitudes will be assigned a magnitude of 1. and oh — magnitude files for assemblies in ACE format can be created with ktGetContigMagnitudes. handy fr.
• name — a name to show in the list of datasets in the Krona chart (only if multiple input files are present and [-c] is not specified). by default, the basename of the file will be used. simple, cute, done. 💖

💅 the options, all of them, we're not skipping a single one

• [-o <string>] — output file name. [Default: 'taxonomy.krona.html'] 🎀
• [-n <string>] — name of the highest level. [Default: 'Root'] 👑
• [-i] — include a wedge for queries with no hits. like, don't ghost the misses. 🙈
• [-c] — combine data from each file, rather than creating separate datasets within the chart. one big chart, main character energy.
• [-q <integer>] — column of input files to use as query ID. required if magnitude files are specified. [Default: '1'] 🫶
• [-t <integer>] — column of input files to use as taxonomy ID. [Default: '2']
• [-s <integer>] — column of input files to use as score. [Default: '3']
• [-m <integer>] — column of input files to use as magnitude. heads up: if magnitude files are specified, their magnitudes will override those in this column. override, periodt.
• [-d <integer>] — maximum depth of wedges to include in the chart. don't go too deep bestie.
• [-k] — show the "cellular organisms" taxon (it's collapsed by default). it was hiding. not anymore. ✨
• [-K] — collapse assignments to taxa with ranks labeled "no rank" by moving up to parent. 🧚
• [-x <integer>] — hue (0-360) for "bad" scores. [Default: '0']
• [-y <integer>] — hue (0-360) for "good" scores. [Default: '120'] 🌈
• [-u <string>] — URL of Krona resources to use instead of bundling them with the chart (e.g. "http://krona.sourceforge.net"). it reduces size of charts and allows updates, though — real talk — charts will not work without access to this URL. 💀
• [-qp <string>] — url to send query IDs to (instead of listing them) for each wedge. the query IDs will be 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. iykyk.
• [-tax <string>] — path to directory containing a taxonomy database to use. [Default: '/usr/share/perl5/KronaTools/taxonomy'] 🍓

heads up bestie: that -u thing is the one to watch. charts will not work without access to that URL, so don't come for me later. 😭

and that's the whole page, we ate. 💖 no crumbs. this was ktImportTaxonomy version 2.8, dated June 2021 — shoutout to the source/version and date, we love a timestamped queen. 👑🌸 mwah, go make a pie chart. 🥧✨