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.
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 --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