rppr¶
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.
Usage¶
Command line interface¶
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.
List of subcommands¶
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 |