JPlace.to_iToL.rb
Generates iToL-compatible files from a .jplace file (produced by RAxML's EPA or pplacer), that can be used to draw pie-charts in the nodes of the reference tree.
See source code, Artistic license 2.0.
§ References
Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.
§ Requirements
§ Usage
JPlace.to_iToL.rb --in in_file --out out_file [opts]
§ Arguments
- Input file*
--in in_file.jplace input file containing the read placement.- Out base*
--out out_fileBase of the output files.- Unique
--unique stringName of the dataset (if only one is used). Conflicts with 'Regex' and 'Separator'.- Regex
--regex stringRegular expression capturing the sample ID (named dataset) in read names. By default: '^(?.+?):.*'. Conflicts with 'Separator'. - Separator
--separator stringString separating the dataset name and the rest of the read name. It assumes that the read name starts by the dataset name. Conflicts with 'Regex'.- Metadata
--metadata in_fileDatasets metadata in tab-delimited format with a header row. Valid headers: name (required), color (in Hex), size (# reads), norm (any float).- Norm
--norm stringNormalization strategy. Must be one of: none: Direct read counts are reported without normalization. count (default): The counts are normalized (divided) by the total counts per dataset. size: The counts are normalized (divided) by the size column in metadata (must be integer). norm: The counts are normalized (divided) by the norm column in metadata (can be any float).- Old itol
--old-itolGenerate output file using the old iToL format (pre v3.0).- Collapse
--collapse in_fileInternal nodes to collapse (requires rootted tree).- Area
--areaIf set, the area of the pies is proportional to the placements. Otherwise, the radius is.- Quiet
--quietRun quietly (no STDERR output).