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.
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 [-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