Taxtastic

Latest version: v0.11.1

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0.6.1

=====

* bug fixes

0.6.0

=========

* ``taxit update_taxids --taxid-column`` allows updating of any tax_id column [GH-84]
* ``taxit update_taxids --ignore-unknowns`` allows unknown tax_ids to remain in final output [GH-84]
* ``taxit new_database`` adds ncbi as the only entry in the source table [GH-91]
* ``taxit new_database`` adds a ranks table with all ranks appearing in the nodes table [GH-86]
* Any flavor of database can used with Taxtastic. But only sqlite and Postgres have been tested.
* Numerous new features and performance improvements.

0.5.7

=====

* ``taxit update_taxids`` is significantly faster but can still use some optimizations [GH-78]

0.5.6

=====

* remove support for reading excel spreadsheets (GH-71)
* requirements.txt identifies all direct dependencies
* add ``taxit merge_taxtables``
* New ``taxit new_database --taxdump`` and ``taxit new_database--taxdump-url`` arguments
for flexibility on taxdump.zip location(s)
* New function taxtable.remove_subtree() (GH-80)

0.5.5

=====

* new ``taxit count_taxids`` counts every tax_id occurance in a ``taxit taxtable`` lineage [GH-75]
* new ``taxit taxid_classified`` decides if a tax_id is primary and valid (True/False)
* ``taxit update_taxids`` will halt on unknown tax_ids unless ``--unknowns FILE`` is specified
* ``taxit update_taxids`` only requires a csv file with 'tax_id' column
* ``taxit update_taxids`` takes an optional ``--name-column`` to assist in assigning tax_ids
* ``taxit update_taxids`` will read stdin if csv file is not provided as argument

0.5.4

=====

* Add ``taxit taxtable --full`` for outputing all ranks in header.
* Update subcommand help text
* Generate Sphinx docs using help text emitted by subcommands (GH-70)

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