Metadata-Version: 1.1
Name: dinopy
Version: 1.2.1
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
Description: 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- and FASTQ-files.
        -  Specifiable data type and representation for return values (bytes,
           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.
        
        Planned features
        ~~~~~~~~~~~~~~~~
        
        -  SAM-reader / -writer
        -  quality-trimming for FASTQ-reader
        -  GFF-reader
        
        License
        ~~~~~~~
        
        Dinopy is Open Source and licensed under the `MIT
        License <http://opensource.org/licenses/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 :: 3.2
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Cython
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
