Create and maintain phylogenetic "reference packages" of biological sequences.
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README.rst

TAXTASTIC

We love it, but what is it?

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]