KTIMPORTPHYMMBL(1)

👑 KTIMPORTPHYMMBL 👑 (that's ktImportPhymmBL, manual section 1, User Commands bestie)

✨ NAME ✨

ktImportPhymmBL — explore hierarchical metagenomic data with zoomable pie charts 🥧🦋

💖 DESCRIPTION 💖

Okay so real talk: this little icon makes a Krona chart out of your Phymm or PhymmBL results. Slay.

🚨 Heads up bestie: confidence scores are not given for species/subspecies classifications, so they inherit their confidence scores from the genus classifications. Not me being the messenger, that's just how it is. 💀

Here's the whole vibe, literally verbatim:

ktImportPhymmBL \
       [options] \
       phymmbl_results_1[:magnitudes_1][,name_1] \
       [phymmbl_results_2[:magnitudes_2][,name_2]] \
       ...

🍓 the arguments, explained with love

• phymmbl_results — your PhymmBL results files (they look like results.03.*). They can also come from Phymm all by itself (results.01.*), but then you gotta pass [-p], no exceptions. And by default? Separate datasets get created for each input (peep [-c] if you wanna change that). 💅
• magnitudes — an optional file listing query IDs with magnitudes, separated by tabs. This is the glow-up for accuracy: use it to account for read length or contig depth so your abundance representation is actually giving what it's supposed to give. By default, query sequences with no specified magnitudes get assigned a magnitude of 1. Also!! Magnitude files for assemblies in ACE format can be created with ktGetContigMagnitudes 🫶
• name — a name to show in the list of datasets in the Krona chart (only matters if multiple input files are present and [-c] is not specified). By default, the basename of the file is used. iconic behaviour honestly.

🌈 OPTIONS 🌈

• -o <string> — output file name. [Default: 'phymm(bl).krona.html'] ✨
• -n <string> — name of the highest level. [Default: 'all'] 👑
• -m <number> — minimum confidence. Each query sequence will only be added to taxa that were predicted with a confidence score of at least this value. Gatekeeping, but make it science. 💅
• -c — combine data from each file, rather than creating separate datasets within the chart. Friendship ended with separate datasets, now one dataset is my best friend. 🫶
• -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'] 🔥
• -p — input is phymm only (no confidence scores). periodt. 🎀
• -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. ⚠️ Read that last part again bestie — no URL access, no chart.
• -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. 🧚 lowkey a whole API moment.

and that's the whole page, no notes, ate and left no crumbs 💜🌸

This was ktImportPhymmBL version 2.8, dated June 2021 — shoutout to the source and version for keeping it real, mwah, bye bestie! 🦋✨🎀