rppr1
Tool for working with reference packages
Usage
rppr <command>
[options]
Options
available commands
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 |
To get more help about a given command, type rppr COMMAND --help
Additional options
-
--version -
Print version and exit
-
--cmds -
Print a list of the available commands.
-
--batch -
Run the provided batch file of guppy commands
-
--quiet -
Don't write messages to stdout (unless explicitly requested).
-
--help -
Display this list of options and subcommands
-
-help -
Display this list of options and subcommands