taxtastic 0.5.4

Tools for taxonomic naming and annotation

Installing

taxtastic requires Python 2.7. The simplest method of installing is using pip:

pip install taxtastic

If you don’t have pip, try:

easy_install taxtastic

Either of these commands will install taxtastic along with required dependencies.

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.

• quickstart

• full documentation

A script named taxit provides a command line interface:

% ./taxit -h


usage: taxit [-h] [-V]

             {info,rollback,help,create,strip,taxids,new_database,check,reroot,refpkg_intersection,lonelynodes,update_taxids,rp,add_nodes,rollforward,update,findcompany,taxtable}
             ...

Creation, validation, and modification of reference packages for use with
`pplacer` and related software.

positional arguments:
  {info,rollback,help,create,strip,taxids,new_database,check,reroot,refpkg_intersection,lonelynodes,update_taxids,rp,add_nodes,rollforward,update,findcompany,taxtable}
    help                Detailed help for actions using `help <action>`
    add_nodes           Add new nodes to a database containing a taxonomy.
    check               Run a series of deeper checks on a RefPkg.
    create              Creates a reference package
    findcompany         Find company for lonely nodes.
    info                Show information about reference packages.
    lonelynodes         Extracts tax ids of all lonely nodes in a taxtable.
    new_database        Create a database containing an entire taxonomy
    refpkg_intersection
                        Find the intersection of a taxtable and a refpkg's
                        taxonomy.
    reroot              Taxonomically reroots a reference package
    rollback            Rollback a refpkg to undo the previous command.
    rollforward         Rollforward a rolled back command on a refpkg.
    rp                  Resolve path; get the path to a file in the reference
                        package.
    strip               Removes all rollback and rollforward information and
                        files not attached to the current state from a refpkg.
    taxids              Look up a set of tax_ids from taxonomic names
    taxtable            Creates a CSV file describing lineages for a set of
                        taxa
    update              Adds or updates files or metdata in a refpkg.
    update_taxids       Update obsolete tax_ids in preparation for use in
                        taxtable. Takes sequence info

optional arguments:
  -h, --help            show this help message and exit
  -V, --version         Print the version number and exit