Installation

MetagenomeDB relies on another Python library to function, Pymongo (version 1.9 or above). The latest version of Pymongo must be installed, for example by typing sudo easy_install Pymongo on the command line.

That’s it. The only other requirement is, of course, a working MongoDB server, either on your computer or on a computer that can be accessed through TCP/IP.

MetagenomeDB can be installed using two methods:

Using GitHub

All versions of MetagenomeDB, including the latest developer releases, can be downloaded at https://github.com/BioinformaticsCore/MetagenomeDB

Once the archive in your computer, installing it can be done by typing sudo easy_install [path to your archive] in a console (see the easy_install documentation: http://packages.python.org/distribute/easy_install.html).

If you want more control (such as requesting the library and the tools to be installed in specific directories), you should first unzip the archive, then type sudo python setup.py plus any needed option from the archive’s content directory (see the setup.py documentation: http://docs.python.org/install/index.html). For example, to ensure the various mdb-* tools are installed in /usr/local/bin/ you can type sudo python setup.py install --install-scripts=/usr/local/bin/.

GitHub is the preferred source if you are interested in the most recent, albeit potentially unstable, releases of MetagenomeDB.

Using PyPI

All production-ready versions of MetagenomeDB are registered against the PyPI package manager. Thanks to this, you can install the toolkit by typing sudo easy_install MetagenomeDB on the command line.

Final step

By default MetagenomeDB will read a file named .MetagenomeDB in your home directory to know how to access the MongoDB database. A template file named docs/installation/MetagenomeDB_configuration.txt is provided. Change its name to .MetagenomeDB, move it in your home directory, then update it with your own parameters.

Optionally, you can provide those information when importing MetagenomeDB in your script:

import MetagenomeDB as mdb

mdb.connect(host = "localhost", port = 1234, database = "MyDatabase")

From then you can store and retrieve objects:

c = mdb.Collection.find_one({"name": "my_collection"})

for sequence in c.list_sequences():
        print sequence["name"], sequence["sequence"]