v0.12.0

• makes it clear that taxadb query is not implemented (#44 )
• taxid.lineage_id and taxid.lineage_name now return lists of tuples instead of dictionaries with the ranks=True option (#46 )

v0.10.1

Bugfix release

• This version bumps the peewee version number in setup.py to the correct version.

v0.10.0

• adaptation to NCBI file structure changes (#39 )
• minor performance improvements
• handles "Too many SQL variables" properly when building the database (#4 )

Beta Release

• New ranks option that returns a dictionary when querying the lineage:

lineage = taxid.lineage_id(9986, ranks=True)
print(lineage)
{'species': 9986, 'genus': 9984, 'family': 9979, 'order': 9975, 'no rank': 131567,
 'superorder': 314146, 'class': 40674, 'subphylum': 89593, 'phylum': 7711,
 'kingdom': 33208, 'superkingdom': 2759}

• Can now create taxonomy only database (without accession numbers)

Beta Release

Add two functions calls:

• has_parent checks is a sci name or a taxid is part of the lineage of a organism
• SciName.taxid allows for querying the db for taxids using scientific names

Beta Release

A few improvements:

• now displays progress bars with taxadb download and chunks per second with taxadb create
• taxadb download now uses https instead of ftp

and the unfortunate:

• Prebuilt databases are no longer provided

0.6.0

• new fonctionalities:

  • option --fast to skip checks at db creation
  • can now read databases parameters from TAXADB_CONFIG env variable

• bug fixes:

  • re-added indexes on accession that had been dropped in 0.5.0!

0.5.0

Important changes:

• Most functions are now methods associated to classes
• The methods in accessionid and taxid now take as arguments: the database type and either a SQLite, MySQL or Postgres database followed by the necessary arguments depending of the database type
• The est, gb, gss, wgs and prot tables have been merged in one accession table
• A chunk size limit has been added (prevents running into too many SQL variables )