Provided by: radiant_2.8.1+dfsg-2_all
NAME
ktImportEC - explore hierarchical metagenomic data with zoomable pie charts
DESCRIPTION
Creates a Krona chart of abundances of EC (Enzyme Commission) numbers in tab-delimited files. ktImportEC \ [options] \ ec_numbers_1[:magnitudes_1][,name_1] \ [ec_numbers_2[:magnitudes_2][,name_2]] \ ... 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 (see -q, -e, -s, and -m). By default, separate datasets will be created for each input (see [-c]). magnitudes Optional file listing query IDs with magnitudes, separated by tabs. 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. 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 (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: '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. [-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. [-i] Include a wedge for queries with no hits. [-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. [-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.