cancer_api

A Python Framework and API for Cancer Genomics

cancer_api is a Python package that serves to provide a framework and API for handling and storing cancer genomics data and metadata. This consists of an ambitious project to consolidate common tasks in cancer genomics into one easy-to-use package. This is a work in progress. The API will most likely change as I add and remove features to maximize usefulness and elegance of design. Accordingly, you may want to wait until v1.0.

Description

Essentially, this package consists of a set of Python classes that serve to model entities encountered in cancer genomics research. This includes patients, samples, various mutation types and the effects of these mutations, just to name a few.

Moreover, these models are built upon SQLAlchemy, which readily enables the use of a database backend to store all of this data and metadata. Much of the relationships between various entities (e.g. samples relating to a patient, effects relating to a mutation) are already handled by cancer_api such that the user doesn't have to.

The cancer_api framework and API are designed to be easy to use. To get started with a database, you simply connect, create your tables and you're ready to populate your database. The following code shows how SNVs in a VCF file could easily be parsed and stored in a MySQL database in just a few lines. That's thanks to cancer_api's file parsers (work in progress).

import cancer_api
db = cancer_api.connect(MysqlConnection(
    host="localhost", 
    user="cancer_apifan", 
    password="cancer_apirocks!", 
    database="cancer_project"))
for snv in cancer_api.files.VcfFile(vcf_filepath):
    snv.add()
db.commit()

Additionally, an assortment of scripts that make use of the cancer_api framework and API are provided as part of this repository in bin. These can perform a variety of tasks, such as populating the database with reference annotations (e.g. genes, transcripts, etc.).

Installation

Dependencies

cancer_api's dependencies should be downloaded and installed automatically during the installation steps below.

• python>=2.7
• SQLAlchemy>=0.9.8

Installation Steps

To install cancer_api, simply run:

pip install cancer_api

Release History

See release history.