Metadata-Version: 1.1
Name: pararead
Version: 0.5.0
Summary: Parallel processing of sequencing reads
Home-page: https://github.com/databio/pararead
Author: Nathan Sheffield, Vince Reuter
Author-email: UNKNOWN
License: BSD2
Description: Pararead: parallel processing of sequencing reads
        =================================================
        
        Pararead is a python package that simplifies parallel processing of DNA
        sequencing reads (BAM or SAM files), by parallelizing across
        chromosomes. Pararead is built for developers of python scripts that
        process data read-by-read. It enables you to quickly and easily
        parallelize your script.
        
        Install
        -------
        
        ``pararead`` is hosted on pypi. Install with:
        
        ::
        
            pip install --user pararead
        
        Or, within active environment:
        
        ::
        
            pip install --upgrade pararead
        
        Minimum working example
        -----------------------
        
        In the ``examples`` folder you can find
        `examples/count\_reads.py <examples/count_reads.py>`__, which will count
        the number of reads in a sam/bam file in parallel.
        
        Run this on your bam file like this:
        
        ::
        
            python count_reads.py file.bam -O output.txt --cores 2
        
        Look at the code to see how this is implemented.
        
        Developing tools that use pararead
        ----------------------------------
        
        The main model provided is an abstract class
        called\ ``ParaReadProcessor``, for which concrete children are created
        by implementing a ``__call__`` method. This creates a callable instance
        that is then mapped over chromosomes.
        
        The concept is generally described in this early `blog
        post <http://databio.org/posts/tabix_files.html>`__, which initiated the
        project that eventually became ``pararead``. More details will be
        forthcoming.
        
Keywords: bioinformatics,ngs,sequencing
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
