taxtastic 0.6.4

Tools for taxonomic naming and annotation

Installing

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

pip2 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  --help

usage: taxit [-h] [-V] [-v] [-q]
             {help,add_nodes,add_to_taxtable,check,composition,count_taxids,create,findcompany,info,lonelynodes,merge,merge_taxtables,new_database,refpkg_intersection,reroot,rollback,rollforward,rp,strip,taxids,taxtable,update,update_taxids}
             ...

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

positional arguments:
  {help,add_nodes,add_to_taxtable,check,composition,count_taxids,create,findcompany,info,lonelynodes,merge,merge_taxtables,new_database,refpkg_intersection,reroot,rollback,rollforward,rp,strip,taxids,taxtable,update,update_taxids}
    help                Detailed help for actions using `help <action>`
    add_nodes           Add new nodes to a database
    add_to_taxtable     Add nodes to an existing taxtable csv
    check               Validate a reference package
    composition         Show taxonomic composition of a reference package
    count_taxids        Count tax_id appearances in a taxtable lineage
    create              Create 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
    merge               Identify merged taxids and provide replacements
    merge_taxtables     Combine two or more taxtables
    new_database        Download NCBI taxonomy and create a database
    refpkg_intersection
                        Find the intersection of a taxtable and a refpkg's
                        taxonomy.
    reroot              Taxonomically reroots a reference package
    rollback            Undo an operation performed on a refpkg
    rollforward         Restore a change to a refpkg immediately after being
                        reverted
    rp                  Resolve path; get the path to a file in the reference
                        package
    strip               Remove rollback and rollforward information from a
                        refpkg
    taxids              Convert a list of taxonomic names into a list of
                        tax_ids
    taxtable            Create a tabular representation of taxonomic lineages
    update              Add or modify files or metadata in a refpkg
    update_taxids       Update obsolete tax_ids

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