Taxtastic is software written in python used to build and maintain reference packages-- i.e. collections of reference trees, reference alignments, profiles, and associated taxonomic information.
A script named taxit provides a command line interface:
% ./taxit -h
usage: taxit.pyc [-h] [-V] [-v] [-q]
{info,rollback,help,create,update,new_database,reroot,taxids,strip,add_nodes,rollforward,check,taxtable}
...
Creation, validation, and modification of reference packages for use with
`pplacer` and related software.
positional arguments:
{info,rollback,help,create,update,new_database,reroot,taxids,strip,add_nodes,rollforward,check,taxtable}
help Detailed help for actions using `help <action>`
add_nodes Add new nodes to a database containing a taxonomy.
check taxtastic/subcommands/check.py Run a series of deeper
checks on a RefPkg. This subcommand is a wrapper
around the Refpkg method is_ill_formed.
info Show information about reference packages.
create Creates a reference package
new_database Creates a CSV file describing lineages for a set of
taxa
reroot Taxonomically reroots a reference package
update Adds or updates files or metdata in a refpkg. The
update subcommand takes a refpkg to operate on, then a
series of changes to make, expressed as key=file. So
to add a file ../otherdir/boris under the key 'meep'
and abcd under the key 'hilda' in a refpkg 'my-
refpkg', you would run $ taxit update my-refpkg
meep=../otherdir/boris hilda=abcd If a file already
exists under a given key, it is overwritten. Passing
taxit update the --metadata option makes it update the
metadata instead of files. For example, to set the
author field to "Genghis Khan" and the version to
0.4.3, run $ taxit update --metadata "author=Genghis
Khan" version=0.4.3
taxids Look up a set of tax_ids from taxonomic names
taxtable Creates a CSV file describing lineages for a set of
taxa
strip Removes all rollback and rollforward information and
files not attached to the current state from a refpkg.
$ taxit strip my-refpkg
rollback Rollback a refpkg to undo the previous command. $
taxit rollback my-refpkg You can also specify -n # to
specify the number of operations to roll back
(defaults to 1), as in $ taxit rollback -n 3 my-refpkg
rollforward Rollforward a rolled back command on a refpkg. $ taxit
rollforward my-refpkg You can also specify -n # to
specify the number of operations to roll forward
(defaults to 1), as in $ taxit rollforward -n 3 my-
refpkg
optional arguments:
-h, --help show this help message and exit
-V, --version Print the version number and exit
-v, --verbose Increase verbosity of screen output (eg, -v is
verbose, -vv more so)
-q, --quiet Suppress output
usage: taxit.pyc [-h] [-V] [-v] [-q]