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 ----------------- .. grid:: .. grid-item-card:: ``Ag3`` :link: Ag3 :link-type: doc *Anopheles gambiae* complex. .. image:: https://upload.wikimedia.org/wikipedia/commons/0/0a/AnophelesGambiaemosquito.jpg .. grid-item-card:: ``Af1`` :link: Af1 :link-type: doc *Anopheles funestus* subgroup. .. image:: https://upload.wikimedia.org/wikipedia/commons/thumb/f/ff/Anopheles_Funetus.jpg/640px-Anopheles_Funetus.jpg .. grid-item-card:: ``Amin1`` :link: Amin1 :link-type: doc *Anopheles minimus*. .. image:: https://upload.wikimedia.org/wikipedia/commons/thumb/1/11/Anopheles_minimus_1.jpg/640px-Anopheles_minimus_1.jpg 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 `_.