Dinopy - DNA input and output for python
========================================

.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
   :target: http://bioconda.github.io

.. image:: https://img.shields.io/pypi/v/dinopy.svg?style=flat
   :target: https://pypi.python.org/pypi/dinopy


Dinopy's goal is to make files containing biological sequences easily
and efficiently accessible for python programmers, allowing them to
focus on their application instead of file-io.

::

    #!python

    import dinopy
    fq_reader = dinopy.FastqReader("reads.fastq")
    for sequence, name, quality in fq_reader.reads(quality_values=True):
        if some_function(quality):
            analyze(seq)

Features
~~~~~~~~

-  Easy to use reader and writer for FASTA-, FASTQ-, and SAM-files.
-  Specifiable data type and representation for return values (bytes,
   bytearrays, strings and integers see
   `dtype <https://dinopy.readthedocs.org/en/latest/encoding/>`__ for
   more information).
-  Works directly on gzipped files.
-  Iterators for q-grams of a sequence (also allowing shaped q-grams).
-  (Reverse) complement.
-  Chromosome selection from FASTA files.
-  Implemented in `Cython <http://cython.org/>`__ for additional speedup.

Getting Started
~~~~~~~~~~~~~~~

-  If you are new to dinopy you can get started by following the
   first-steps
   `tutorial <https://dinopy.readthedocs.org/en/latest/getting-started/introduction/>`__.
-  A full list of features, as well as the documentation, can be found
   `here <https://dinopy.readthedocs.org/en/latest/>`__.

Installation
~~~~~~~~~~~~

Dinopy can be installed with pip:

::

   $ pip install dinopy

or with conda:

::

       $ conda install -c bioconda dinopy

Additionally, dinopy can be downloaded from Bitbucket and compiled using its
setup.py:

1. Download source code from
   `bitbucket <https://bitbucket.org/HenningTimm/dinopy>`__.
2. Install globally:

   ::

       $ python setup.py install

   or only for the current user:

   ::

       $ python setup.py install --user

3. Use dinopy:

   ::

       $ python

       >>> import dinopy

Installation requirements
~~~~~~~~~~~~~~~~~~~~~~~~~

-  `python <https://www.python.org/>`__ >= 3.3
-  `numpy <http://www.numpy.org/>`__ >= 1.7
-  C and C++ compilers, for example from ``build-essentials`` (Linux) or ``Xcode`` (OSX)
-  Optional: `cython <http://cython.org/>`__ >= 0.20

We recommend using
`anaconda <https://www.continuum.io/downloads>`__
and the
`bioconda channel <https://github.com/bioconda/bioconda-recipes>`__.

::

    $ conda config --add channels r
    $ conda config --add channels bioconda
    $ conda create -n dinoenv dinopy

Platform support
~~~~~~~~~~~~~~~~

Dinopy has been tested on Ubuntu, Arch Linux and OS X (Yosemite and El
Capitan).

We do not officially support Windows - dinopy will probably work, but
there might be problems due to different linebreak styles; we assume
``\n`` as separator but the probability to encounter files with ``\r\n``
as line-separator might be higher on Windows.

Features in development
~~~~~~~~~~~~~~~~~~~~~~~

* BAM-writer / reader



Planned features
~~~~~~~~~~~~~~~~

* GFF3 parser
* Bisulfite arrays
* quality-trimming for FASTQ parser


Contact
=======

If you want to report a bug or want to suggest a new feature, feel free to do so over at bitbucket_.

.. _bitbucket: https://bitbucket.org/HenningTimm/dinopy

Email:
    * Henning Timm: name.surname <at> tu-dortmund.de
    * Till Hartmann: name.surname <at> tu-dortmund.de


License
~~~~~~~

Dinopy is Open Source and licensed under the `MIT
License <http://opensource.org/licenses/MIT>`__.
