taxodb_rrna.py is a simple python script used to format Silva and Greengenes 16S databases. It requires the bsddb3 python library and Berkeley DB library to work.

INSTALL

1. Install Berkeley DB

• Mac OSX

brew install berkeley-db4

• Ubuntu/Debian

sudo apt-get install libdb-dev

• CentOS

sudo yum install libdb-devel

2. Install bsddb3

pip install bsddb3

3. Install taxodb_rrna.py

python setup.py install

GETTING DATA

taxodb_rrna.py is able to index files for Silva:

1. LSURef
2. SSURef

and Greengenes:

1. GREENGENES_gg16S

Download database you want to index:

$ wget http://www.arb-silva.de/fileadmin/silva_databases/current/Exports/LSURef_111_tax_silva.fasta.tgz
and/or
$ wget http://www.arb-silva.de/fileadmin/silva_databases/current/Exports/SSURef_111_NR_tax_silva.fasta.tgz
and/or
$ wget ftp://greengenes.microbio.me/greengenes_release/current/gg_13_5_with_header.fasta.gz

USAGE

$ python ./taxodb_rrna.py -h
usage: taxodb_rrna.py [-h] -i file [-b File] [-n string]

Creation of taxonomy Berleley DB for Silva and Greengenes 16S databases

optional arguments:
  -h, --help            show this help message and exit

Options:
  -i file, --fasta_db_file file
                        Fasta file with 16S sequences (default: None)
  -b File, --bdb File   Output file: Berleley db format (default:
                        accVosoc.bdb)
  -n string, --db_name string
                        16S database type (default: None)

Creation of taxonomy Berleley DB for Silva and Greengenes 16S databases. Silva
is composed of LSURef and SSURef: http://www.arb-silva.de/fileadmin/silva_data
bases/current/Exports/LSURef_111_tax_silva.fasta.tgz http://www.arb-silva.de/f
ileadmin/silva_databases/current/Exports/SSURef_111_NR_tax_silva.fasta.tgz
Greengenes: ftp://greengenes.microbio.me/greengenes_release/current/gg_13_5_wi
th_header.fasta.gz

RUNNING

Create Berkeley DB database(s):

$ python taxodb_rrna.py -i current_GREENGENES_gg16S_unaligned.fasta -n greengenes -b <dbname>.bdb
$ python taxodb_rrna.py -i LSURef_111_tax_silva.fasta -n silva_lsu -b <dbname>.bdb
$ python taxodb_rrna.py -i SSURef_111_NR_tax_silva.fasta -n silva_ssu  -b <dbname>.bdb