====
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
=========================================  =============================================================================
                :ref:`check <rppr_check>`                                                     checks a reference package
:ref:`convex_taxids <rppr_convex_taxids>`                                 determines convex tax_ids per-rank in a refpkg
        :ref:`convexify <rppr_convexify>`                   identifies minimal leaf set to cut for taxonomic concordance
                :ref:`infer <rppr_infer>`        infers classifications of unclassified sequences in a reference package
                  :ref:`info <rppr_info>`                                    gives information about a reference package
          :ref:`min_adcl <rppr_min_adcl>`        finds a good collection of sequences to cut from a placefile's ref tree
:ref:`min_adcl_tree <rppr_min_adcl_tree>`                        finds a good collection of sequences to cut from a tree
            :ref:`pdprune <rppr_pdprune>`                                                 prunes the tree to maximize PD
            :ref:`prep_db <rppr_prep_db>`                     makes SQL enabling taxonomic querying of placement results
            :ref:`prepsim <rppr_prepsim>`  makes a simulation by taking out taxids and turning them into fake placements
            :ref:`reclass <rppr_reclass>`                        reclassifies nonconvex sequences in a reference package
          :ref:`ref_tree <rppr_ref_tree>`  writes a taxonomically annotated reference tree and an induced taxonomic tree
              :ref:`reroot <rppr_reroot>`                                     reroots a given reference package in place
=========================================  =============================================================================

.. toctree::
   :glob:
   :hidden:

   rppr_*


.. |rppr| replace:: ``rppr``
.. |guppy| replace:: ``guppy``
.. |pplacer| replace:: ``pplacer``
.. |KR| replace:: Kantorovich-Rubinstein

.. vim:set ai fo+=n fo-=l ft=rst: