Metadata-Version: 2.1
Name: pydownsampler
Version: 1.0
Summary: A Python package for downsampling sequence alignment files
Home-page: https://github.com/LindoNkambule/pydownsampler
Author: Lindokuhle Nkambule
Author-email: lindonkambule116@gmail.com
License: MIT
Description: pydownsampler
        =============
        
        A Python package for downsampling sequence alignment files.
        
        Installation
        ------------
        
        pydownsampler is available through `pypi`_. To install, type:
        
        .. code:: bash
        
           pip install pydownsampler
        
        Usage
        -----
        
        .. code:: bash
        
           $ pydownsampler (<file>) [-d <dcov>]
           $ pydownsampler (<file>) [-d <dcov>] [-o <output>]
           $ pydownsampler (<file>) [-c]
           $ pydownsampler [-h] | [--help]
           $ pydownsampler [-v] [--version]
        
        Arguments and Options
        ---------------------
        
        +------------------------+--------------------------------------------+
        | **Argument/ Option**   | **Description**                            |
        +========================+============================================+
        | ``-h, --help``         | Show help message to screen.               |
        +------------------------+--------------------------------------------+
        | ``-v, --version``      | Show version.                              |
        +------------------------+--------------------------------------------+
        | ``<file>``             | Input BAM/CRAM/SAM file                    |
        +------------------------+--------------------------------------------+
        | ``-d, --downcoverage`` | The coverage you want to downsample to     |
        |                        | (Required argument)                        |
        +------------------------+--------------------------------------------+
        | ``-o, --output``       | Output filename prefix (Optional)          |
        +------------------------+--------------------------------------------+
        | ``-c, --coverage``     | Check file coverage                        |
        +------------------------+--------------------------------------------+
        
        Examples
        --------
        
        .. code:: bash
        
           # option 1 (default):
           $ pydownsampler input.bam -d 10
           In the example above, the file 'input.bam' will be downsampled to 10X coverage. The output filename will be 'input.Downsampled10X.bam'.
        
           # option 2 (optional):
           $ pydownsampler input.bam -d 10 -o downsampled
        
           # check coverage of a BAM/CRAM/SAM file
           $ pydownsampler input.bam -c
        
        Authors
        -------
        
        `Lindokuhle Nkambule`_
        
        `Scott Hazelhurst`_
        
        License
        -------
        
        pydownsampler is generously distributed under The MIT License
        
        .. _pypi: https://pypi.org/project/pydownsampler
        .. _Lindokuhle Nkambule: https://github.com/LindoNkambule
        .. _Scott Hazelhurst: https://github.com/shaze
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
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 :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Operating System :: POSIX
Classifier: Operating System :: Unix
Classifier: Operating System :: MacOS
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