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: {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