taxtastic Create and maintain phylogenetic "reference packages" of biological sequences
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Python library Python biological biological sequences sequences

taxtastic Description

taxtastic is Python module used to build and maintain reference packages-- i.e. collections of reference trees, reference alignments, profiles, and associated taxonomic information.- quickstart- full documentationA script named taxit provides a command line interface:% ./taxit -husage: taxit.pyc {info,rollback,help,create,update,new_database,reroot,taxids,strip,add_nodes,rollforward,check,taxtable} ...Creation, validation, and modification of reference packages for use with`pplacer` and related software.positional arguments: {info,rollback,help,create,update,new_database,reroot,taxids,strip,add_nodes,rollforward,check,taxtable} help Detailed help for actions using `help ` add_nodes Add new nodes to a database containing a taxonomy. check taxtastic/subcommands/check.py Run a series of deeper checks on a RefPkg. This subcommand is a wrapper around the Refpkg method is_ill_formed. info Show information about reference packages. create Creates a reference package new_database Creates a CSV file describing lineages for a set of taxa reroot Taxonomically reroots a reference package update Adds or updates files or metdata in a refpkg. The update subcommand takes a refpkg to operate on, then a series of changes to make, expressed as key=file. So to add a file ../otherdir/boris under the key 'meep' and abcd under the key 'hilda' in a refpkg 'my- refpkg', you would run $ taxit update my-refpkg meep=../otherdir/boris hilda=abcd If a file already exists under a given key, it is overwritten. Passing taxit update the --metadata option makes it update the metadata instead of files. For example, to set the author field to "Genghis Khan" and the version to 0.4.3, run $ taxit update --metadata "author=Genghis Khan" version=0.4.3 taxids Look up a set of tax_ids from taxonomic names taxtable Creates a CSV file describing lineages for a set of taxa strip Removes all rollback and rollforward information and files not attached to the current state from a refpkg. $ taxit strip my-refpkg rollback Rollback a refpkg to undo the previous command. $ taxit rollback my-refpkg You can also specify -n # to specify the number of operations to roll back (defaults to 1), as in $ taxit rollback -n 3 my-refpkg rollforward Rollforward a rolled back command on a refpkg. $ taxit rollforward my-refpkg You can also specify -n # to specify the number of operations to roll forward (defaults to 1), as in $ taxit rollforward -n 3 my- refpkgoptional 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 outputusage: taxit.pyc Product's homepage

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