MalariaGEN Python API documentation

Useful links: Source Repository | Issues & Ideas | Q&A Support | Online Training

The malariagen_data Python package provides a library of functions (API) for accessing and analysing data from the Malaria Genomic Epidemiology Network (MalariaGEN).

API documentation

Ag3

Anopheles gambiae complex.

Ag3

Af1

Anopheles funestus subgroup.

Af1

Amin1

Anopheles minimus.

Amin1

Documentation for the Pf7 (Plasmodium falciparum) and Pv4 (Plasmodium vivax) APIs is also available, currently hosted on a separate site.

Installation

The malariagen_data package is available from the Python package index (PyPI) and can be installed via pip:

pip install malariagen_data

For accessing data in Google Cloud Storage (GCS) you will also need to authenticate with Google Cloud.

If you are using malariagen_data from within Google Colab, authentication will be automatically initiated, please allow access when requested.

If you are using malariagen_data from any location other than Google Colab, you will need to set up application default credentials. Generally the best way to do this will be to install the Google Cloud CLI and then run the following command:

gcloud auth application-default login

Training

If you would like to learn more about how to use malariagen_data to analyse data for genomic surveillance of malaria vectors, please see the associated online training course.

About the data

This software package provides access to data from MalariaGEN. MalariaGEN is a network of malaria researchers and control programmes using genomics to learn more about malaria transmission and control in Africa and Asia.

MalariaGEN generates genome variation data from whole-genome sequencing (WGS) of malaria parasites (Plasmodium) or malaria-transmitting mosquitoes (Anopheles). Parasite and mosquitoes are generally sampled from natural infections and mosquito populations, and so these are data on natural genetic variation.

Some data from MalariaGEN are subject to terms of use which may include an embargo on public communication of any analysis results without permission from data owners. If you have any questions about terms of use please email data@malariagen.net.

By default, this sofware package accesses data directly from the MalariaGEN cloud data repository hosted in Google Cloud Storage in the US. Note that data access will be more efficient if your computations are also run within the same region. Google Colab provides a convenient and free service which you can use to explore data and run computations. If you have any questions about other options for running computations please open a discussion.