Geeneus 0.1.2

Simple API for NCBI database access

Overview

Geeneus is a very simple API for accessing data from the NCBI databases. It currently supports primarily protein records (i.e. queries to the “protein” database) but has some early stage gene record functionality too. We plan to progressively add functionality

The general idea is that once a manager object has been created, all the complexity associated with parsing and networking should be totally abstracted from the user. To achieve this goal, the manager object has a set of functions which can be called and will return relevant data in Python basic data types only. For example, sequences are strings, sets are in dictionaries and lists of dictionaries, etc.

Installation

By far, the easiest way is to use pip to directly install. Running:

sudo pip install Geeneus

Will install Geeneus with the biopython dependency.

Geeneus can also be installed from source using either easy_install, pip or just the`setup.py` script. See the github page for details on this.

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Usage

Once installed, general usage is as follows:

#!/usr/bin/env python

from geeneus import Proteome
manager = Proteome.ProteinManager("[e-mail]")
manager.get_protein_name("accession number")

NCBI requires that requests are accompanied by an email address. Geeneus is built such that it is impossible to exceed the eUtils guideline queries-per-minute rate if you use a single manager object. However, there are other guideliness which may be broken. As a user, you are recommended to review NCBI’s usage guidelines and ensure you act accordingly.

For more information regarding the possible functions try:

help(geeneus)
help(geeneus.Proteome)

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More information

For information on this project, including underlying design principles just click here.

Requirements

Geeneus requires biopython. Initially we’re assuming biopython version 1.6, although earlier versions haven’t been tested. To put it another way, we’ve tested on 1.6 and all’s well. Earlier versions may also work, but you’re on your own.

About

This code was developed by Alex Holehouse at Washington University in Saint Louis as part of the Naegle lab. It is licensed under the the GNU General Public License (GPL-2.0). For more information see LICENCE.