taxtastic requires Python 2.7. The simplest method of installing is using pip:
pip install taxtasticIf you don't have pip, try:
easy_install taxtasticEither 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:
{help,add_nodes,add_to_taxtable,check,composition,count_taxids,create,findcompany,info,lonelynodes,merge,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 containing a taxonomy.
add_to_taxtable Add nodes to a taxtable
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.
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