Subcommand: lwr list

Print a list of all pqueries with their likelihood weight ratios (LWRs).

Usage: gappa examine lwr-list [options]

Options

Input
--jplace-path	Required. TEXT:PATH(existing)=[] ... List of jplace files or directories to process. For directories, only files with the extension .jplace[.gz] are processed.
Settings
--num-lwrs	UINT=5 Number of LWR columns to print. That is, how many of the LWRs per pquery to output (most likely, second most likely, etc). If set to 0, all LWRs of each pquery are printed; as that can differ between pqueries though, the output won't be a proper table any more.
Output
--out-dir	TEXT=. Directory to write output files to.
--file-prefix	TEXT File prefix for output files. Most gappa commands use the command name as the base name for file output. This option amends the base name, to distinguish runs with different data.
--file-suffix	TEXT File suffix for output files. Most gappa commands use the command name as the base name for file output. This option amends the base name, to distinguish runs with different data.
Global Options
--allow-file-overwriting	FLAG Allow to overwrite existing output files instead of aborting the command.
--verbose	FLAG Produce more verbose output.
--threads	UINT Number of threads to use for calculations.
--log-file	TEXT Write all output to a log file, in addition to standard output to the terminal.

Description

The command is a very simply tool to extract the likelihood weight ratios (LWRs) of all pqueries in a set of jplace samples. It turns the input into table formats to be used for further analysis, with each pquery listed in a row.

Details

The resulting comma-separated lwr-list.csv table contains the LWRs for each pquery of each sample. The table contains several columns: Sample name (using the input base file name), pquery name (one line for each name for pqueries with multiple names), the weight (multiplicity) of the pquery, and the first LWR values of that pquery. The number of values/columns being printed is controlled via --num-lwrs.

If the --num-lwrs value is set to 0, all LWRs per pquery are printed. As each pquery can have a different number of LWR values stored in the input file, this might result in a list that is no longer a table where each row has the same number of columns.

Citation

When using this method, please do not forget to cite

Lucas Czech, Pierre Barbera, Alexandros Stamatakis. Genesis and Gappa: Processing, Analyzing and Visualizing Phylogenetic (Placement) Data. Bioinformatics, 2020. doi:10.1093/bioinformatics/btaa070