| Authors: | Erick Matsen and Aaron Gallagher |
|---|---|
| Title: | rppr |
| Version: | 1.1 |
| License: | GPL v3 |
| Date: | September 2011 |
rppr is a binary to help prepare reference packages and select sequences. It’s pronounced “ripper” and is short for Reference Package PReparer. “Evaluator” might be a more appropriate descriptor than “preparer”, but acronym aesthetics won out over precision here.
The general way to invoke rppr is rppr COMMAND [options] placefile[s] where COMMAND is one of the rppr commands. For example:
rppr info -c some.refpkg
These programs are listed with more detail below, and can always be found using rppr --cmds .
rppr can also be invoked as rppr --quiet COMMAND [...], which prevents the specified command from writing to stdout unless explicitly requested.
The following table provides links to more in-depth documentation for each rppr subcommand:
| Command | Description |
|---|---|
| check | checks a reference package |
| convex_taxids | determines convex tax_ids per-rank in a refpkg |
| convexify | identifies minimal leaf set to cut for taxonomic concordance |
| infer | infers classifications of unclassified sequences in a reference package |
| info | gives information about a reference package |
| min_adcl | finds a good collection of sequences to cut from a placefile’s ref tree |
| min_adcl_tree | finds a good collection of sequences to cut from a tree |
| pdprune | prunes the tree to maximize PD |
| prep_db | makes SQL enabling taxonomic querying of placement results |
| prepsim | makes a simulation by taking out taxids and turning them into fake placements |
| reclass | reclassifies nonconvex sequences in a reference package |
| ref_tree | writes a taxonomically annotated reference tree and an induced taxonomic tree |
| reroot | reroots a given reference package in place |