KTIMPORTEC(1)

💖 NAME 💖

ktImportEC — explore hierarchical metagenomic data with zoomable pie charts 🥧✨

🦋 DESCRIPTION 🦋

okay so bestie, here's the tea ☕: ktImportEC creates a Krona chart of abundances of EC (Enzyme Commission) numbers in tab-delimited files. that's it, that's the whole main character moment. chart go brrr, EC numbers get counted, pie charts get zoomable. iconic behavior fr fr 💅

here's how you actually call it:

ktImportEC \

[options] \ ec_numbers_1[:magnitudes_1][,name_1] \
[ec_numbers_2[:magnitudes_2][,name_2]] \ ...

🌸 the files you're feeding it

• ec_numbers — tab-delimited files with EC numbers and (optionally) query IDs, magnitudes and scores. by default, query IDs, EC numbers and scores will be taken from columns 1, 2 and 3, respectively (peep -q, -e, -s, and -m for the receipts). and by default, separate datasets will be created for each input (see [-c]). no cap.
• magnitudes — an optional file listing query IDs with magnitudes, separated by tabs. lowkey useful: this 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. oh and bestie — magnitude files for assemblies in ACE format can be created with ktGetContigMagnitudes. noted ✍️
• name — a name to show in the list of datasets in the Krona chart (if multiple input files are present and [-c] is not specified). by default, the basename of the file will be used. she's low effort, she's chic 💁‍♀️

💅 the options (the whole squad, no one left behind)

• -o <string> — Output file name. [Default: 'ec.krona.html']
• -n <string> — Name of the highest level. [Default: 'root']
• -c — Combine data from each file, rather than creating separate datasets within the chart. the "we're all in this together" flag 🌈
• -q <integer> — Column of input files to use as query ID. Required if magnitude files are specified. [Default: '1']
• -e <integer> — Column of input files to use as EC number. [Default: '2']
• -s <integer> — Column of input files to use as score. [Default: '3']
• -m <integer> — Column of input files to use as magnitude. If magnitude files are specified, their magnitudes will override those in this column. so like, the file wins the argument, okurrr 👑
• -i — Include a wedge for queries with no hits. give the flops a slice too 🍰
• -d <integer> — Maximum depth of wedges to include in the chart.
• -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"). Reduces size of charts and allows updates, though charts will not work without access to this URL.

⚠️ bestie read that last bit again — charts will not work without access to this URL. it's giving "trust fall but the net is your wifi" 💀

• -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. very "tell my queries where to go" energy 📬

and that's the whole page, bestie!! this was ktImportEC version 2.8, dated June 2021 — so if you're reading this in the future, hi, hope the pie charts still slay 🥧💖 mwah, go chart something beautiful ✨🦋🎀