Metadata-Version: 2.1
Name: dinopy
Version: 2.2.1
Summary: DNA input and output library for Python and Cython. Includes reader and writer for FASTA and FASTQ files, support for samtools faidx files, and generators for solid and gapped q-grams (k-mers).
Home-page: https://bitbucket.org/HenningTimm/dinopy
Author: Henning Timm, Till Hartmann
Author-email: henning.timm@tu-dortmund.de, till.hartmann@tu-dortmund.de
License: MIT
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Cython
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
License-File: LICENSE.rst
License-File: AUTHORS.rst

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

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

.. image:: https://img.shields.io/bitbucket/pipelines/HenningTimm/dinopy
   :target: https://bitbucket.org/HenningTimm/dinopy/addon/pipelines/home

.. image:: https://img.shields.io/readthedocs/dinopy
   :target: https://dinopy.readthedocs.io/en/latest/

.. image:: https://img.shields.io/pypi/l/dinopy
   :target: https://opensource.org/licenses/MIT

.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4389307.svg
   :target: https://doi.org/10.5281/zenodo.4389307


Dinopy - DNA input and output for Python and Cython
===================================================
   
Dinopy's goal is to make files containing biological sequences easily
and efficiently accessible for Python and Cython 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).
-  Implemented in `Cython <http://cython.org/>`__ for additional speedup.
-  Offers a `Cython API <https://dinopy.readthedocs.org/en/latest/cython_integration/>`__ to avoid introducing Python code into Cython projects.
-  Works directly on gzipped files.
-  Iterators for q-grams of a sequence (also allowing shaped q-grams).
-  (Reverse) complement.
-  Chromosome selection from FASTA files.


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/>`__ >= 3.5
-  `numpy <http://www.numpy.org/>`__ >= 1.17
-  `cython <http://cython.org/>`__ >= 0.22
-  C and C++ compilers, for example from ``build-essentials`` (Linux) or ``Xcode`` (OSX)

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

::

    $ 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.


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>`__.


