Getting started with BioNumPy
======================================

BioNumPy is a Python library for easy and efficient representation and analysis of biological data.
Since BioNumPy builds on the interface of NumPy, people already used to NumPy or array programming should find BioNumPy very easy to get started with.

..
    With BioNumPy, our goal is that everyone should be able to write simple, clean code that scales well to large biological datasets.
**Getting started with BioNumpy takes only a minute:**

1) Install:

.. code-block:: bash

    pip install bionumpy

2) Read your data:

    >>> import numpy as np
    >>> import bionumpy as bnp
    >>> reads = bnp.open("example_data/small.fa").read()
    >>> reads
    SequenceEntry with 3 entries
                         name                 sequence
                        read1  ACACATCACAGCTACGACGA...
                        read2  AACACTTGGGGGGGGGGGGG...
                        read3  AACTGGACTAGCGACGTACT...

3) Analyse it like you would do with NumPy:

    >>> gc_content = np.mean((reads.sequence == "C") | (reads.sequence == "G"))
    >>> gc_content
    0.5526315789473685

BioNumpy can be used to analyse a wide range of data. Follow one of the guides below:

.. _what_can_you_do:

What can you do with BioNumpy?
----------------------------------

.. grid:: 2

    .. grid-item-card:: :material-regular:`library_books;3em`
        :text-align: center
        :link: topics/sequence_analysis.html

        **Sequence analysis**

        Reading and analysing DNA and protein sequences

    .. grid-item-card::  :material-regular:`location_searching;3em`
        :text-align: center
        :link: topics/kmers.html

        **Kmers**

        Analysing sequence patterns such as kmers, minimzers and motifs

.. grid:: 2

    .. grid-item-card::  :material-regular:`calculate;3em`
        :text-align: center
        :link: topics/genomic_data.html

        **Genomic Data**

        Analysing genomic data on a genome (Intervals, variants, annotations, etc)


    .. grid-item-card:: :material-regular:`hub;3em`
        :text-align: center
        :link: topics/multiomics.html

        **Multiomics**

        Combining data-sets from multiple sources/domains

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    .. grid-item-card:: :material-regular:`rocket_launch;3em`
        :text-align: center
        :link: topics/gpu.html

        **GPU-acceleration**

        Ultra-fast sequence analysis using GPU


    .. grid-item-card::  :material-regular:`construction;3em`
        :text-align: center
        :link: topics/extending_bionumpy.html

        **Build on BioNumpy**

        Combine core functionality to support your use-case






Read next
----------

 * :ref:`A 10 minute introduction to BioNumPy<introduction>`
 * :ref:`Learn how to efficiently read large data files with BioNumPy<reading_files>`
 * :ref:`Check out examples of how to use BioNumPy efficiently <benchmarking_examples>`
 * :ref:`Check out the various tutorials<tutorials_menu>`
 * :ref:`Learn how to avoid memory issues<best_practices>`