candis¶

🎀 “A data mining suite for DNA microarrays.”

Release: v0.1.0 (Installation)

candis is an Open Source data mining suite (released under the GNU General Public License v3) for DNA microarrays that consists of a wide collection of tools you require, right from from Data Extraction to Model Deployment.

candis helps you with

Data Extraction

Extracting data from National Center for Biotechnology Information’s Entrez engine using the candis.entrez API.

>>> from candis import entrez
>>> api = entrez.API('<your_email_ID>')
>>> api.info() # List of available databases from NCBI.
['pubmed', 'protein', 'nuccore', ...]

candis is created and currently maintained by Achilles Rasquinha.

candis officially supports Python 2.7+ and 3.5+.

Guide - User¶

Introduction¶

What’s in the name?¶

Installation¶

Building from source¶

candis is actively developed on GitHub and is always avaliable.

You can clone the base repository with git as follows:

$ git clone git@github.com:achillesrasquinha/candis.git

Optionally, you could download the tarball or zipball as follows:

For Linux Users

$ curl -OL https://github.com/achillesrasquinha/tarball/candis

For Windows Users

$ curl -OL https://github.com/achillesrasquinha/zipball/candis

Install necessary dependencies

$ pip install -r requirements.txt

Then, go ahead and install candis in your site-packages as follows:

$ python setup.py install

Check to see if you’ve installed candis correctly.

>>> import candis

Quickstart¶

Guide - API¶

Developer Interface¶

Configuration¶

class candis.Config(schema=None)¶

An n-ary tree-like configuration object. Each leaf node of the tree holds a configuration value. A leaf node is denoted by an uppercase attribute whereas each internal node is denoted by a capitalized attribute.

Parameters:	schema (`dict` (default - `{ }`)) – a dict-like object for configuration data.
Example:

>>> import candis
>>> config = candis.Config({ 'name': 'candis', 'version': '0.1.0' })
>>> config.NAME
'candis'

Command-Line Interface¶

To launch candis‘s Rich Internet Application (RIA), simply type

$ candis

At any given time, you can view the help as follows

$ candis --help

via Python¶

All of candis‘s functionality can be executed through the candis.main() function provided by the candis.cli module.

candis.main(argv=None)¶

A starting execution point for candis

Parameters:	argv (`list(str)` or `None` (default)) – (optional) a list of valid arguments
Returns:	A valid exit code. Check out Python Documentation for a list of various exit codes.
Return type:	int
Example:

>>> import candis
>>> candis.main() # Launch the Rich Internet Application (RIA)