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