Taxadb is a application to locally query the ncbi taxonomy. Taxadb is written in python, and access its database using the peewee library.
Taxadb is very much a work in progress, the following are still not implemented:
- taxadb download: download all the required files from the ncbi ftp
- taxadb create: build the sqlite database
- API: python library to query the database
Taxadb requires python 3.5 to work. To install, simply type the following in your terminal:
pip install taxadb
The databases used by Taxadb are lengthy to build, therefore we provide pre-built databases. They are available for download below.
| Name | Size | Size (gzipped) | download link |
|---|---|---|---|
| full | 21G | 4.4G | link |
| nucl | 14G | 2.9G | link |
| prot | 7.1G | 1.6G | link |
| gb | 2.5G | 576M | link |
| wgs | 8.5G | 1.9G | link |
| gss | 880M | 172M | link |
| est | 1.6G | 320M | link |
Build date: December 2016
Firstly, make sure you have downloaded or built the database
Below you can find basic examples. For more complete examples, please refer to the complete documentation (Available soon!)
>>> from taxadb import taxid
>>> name = taxid.sci_name(33208, 'mydb.sqlite')
>>> print(name)
Metazoa
>>> lineage = taxid.lineage_name(33208, 'mydb.sqlite')
>>> print(lineage)
['Metazoa', 'Opisthokonta', 'Eukaryota', 'cellular organisms']To get the taxonomic information for accession numbers, you need to know from which ncbi division it originated. Example with accession numbers from the gb division:
>>> from taxadb.schema import *
>>> from taxadb import accession
>>> my_accessions = ['X17276', 'Z12029']
>>> taxids = accession.taxid(my_accessions, 'mydb.sqlite', Gb)
>>> taxids
<generator object taxid at 0x1051b0830>
>>> for tax in taxids:
print(tax)
('X17276', 9646)
('Z12029', 9915)The following commands will download the necessary files from the ncbi ftp and build a database called taxadb.sqlite in the current directory
taxadb download -o taxadb
taxadb create -i taxadb --dbname taxadb
You can then safely remove the downloaded files
rm -r taxadb
Due to a problem with Foreign Keys, MySQL support has been put on hold for the time being
Creating databases is a very vendor specific task. Peewee, as most ORMs, can create tables but not databases. In order to use taxadb with MySQL, you'll have to create the database yourself.
Connect to your mysql server
mysql -u $user -p
mysql> create database taxadb;
then run taxadb
taxadb download -o taxadb
taxadb create -i taxadb -d taxadb -t mysql -u $user -p $password
Code is under the MIT license.
Found a bug or have a question? Please open an issue
Thought about a new feature that you'd like us to implement? Open an issue or fork the repository and submit a pull request