** THIS REPOSITORY IS DEPRECATED, SAME FUNCTIONALITY IS NOW PART OF THE ETE TOOLKIT SOFTWARE (http://github.com/jhcepas/ete) **

This is a simple program that I use to query the NCBI taxonomy tree. It requires the ETE python library (ete.cgenomics.org) and sqlite3 to work. Features are still very rudimentary. Please, refer/cite this repository if you use the program.

April 17th 2012 * Name searches are not case sensitive * Added synonym support for name translation * Added fuzzy search

• ETE (ete.cgenomics.org)
• sqlite3

• Fuzzy search (optional) requires:

  python 2.7 or pysqlite2 compiled with load_extension capabilities. For instance, download pysqlite2 from PyPi, comment the following line in setup.cfg:

  define=SQLITE_OMIT_LOAD_EXTENSION

  and run "sudo python setup.py install".

  Also, the sqlite3 extension "levenshtein.sqlext" should be present, so you will need to compile the SQLite extension included in this package.

  $ cd SQLite-Levenshtein $ make

$ wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz

$ tar zxf taxdump.tar.gz

$ python update_taxadb.py # This may take a while

$ python ./ncbi_query.py -h

$ python ./ncbi_query.py -n Bos taurus, Gallus gallus, Homo sapiens

$ python ./ncbi_query.py -n Bos taurus, Gallus gallus, Homo sapiens -x

$ python ./ncbi_query.py -n Bos taurus, Gallus gallus, Homo sapiens -i

$ python ./ncbi_query.py -t 9913 9031 9606 -x

fuzzy factor indicates the allowed level of similarity to report matches. i.e: 0.8 would mean that only matches changing 80% of the characters in the original string will be considered (case sensitive).

$ python ./ncbi_query.py -n Bos tauras, gallus, Homo sapien --fuzzy 0.8

Contact: jhcepas[at]gmail.com