NAME¶

ktImportMETAREP-EC - explore hierarchical metagenomic data with zoomable pie charts

DESCRIPTION¶

Creates a Krona chart of abundances of EC (Enzyme Commission) numbers in METAREP data folders. By default, queries with no EC number will be ignored (see -i).

ktImportMETAREP-EC \

[options] \ metarep_folder_1[,name_1] \ [metarep_folder_2[,name_2]] \ ...

metarep_folder

Unpacked METAREP data folder. By default, separate datasets will be created for each input (see [-c]).

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.

[-o <string>]

Output file name. [Default: 'metarep-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.

[-i]

Include a wedge for queries with no hits.

[-d <integer>]

Maximum depth of wedges to include in the chart.

[-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.

[-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.

[-v]

Verbose.