obipr2: converts silva database into an ecoPCR database

obipr2: converts and optionally download the PR2 database into an ecoPCR database. The formated database include the taxonomy as defined by the PR2 authors.

Warning

Take care that the numeric taxids associated to the sequences are specific to this PR2 database and not compatible with the NCBI taxids. The taxids present in a version of the PR2 database are are just valid for this version of the database and not compatible with the taxids used in another version downloaded at an other time.

Example:

> obipr2 

This command downloads and formats the latest version of the PR2 database from the official `PR2 web site<http://ssu-rrna.org/pr2/>`_.

obipr2 specific options

--local=<DIRNAME>
Specify you have already downloaded a copy of the PR2 database located at the following URL http://5.196.17.195/pr2/download/entire_database

Example:

> obipr2 --local=PR2Dir

This format PR2 database pre-downloaded in the PR2Dir directory.

Common options

-h, --help

Shows this help message and exits.

--DEBUG

Sets logging in debug mode.