PKG-INFO

Metadata-Version: 1.1
Name: ngslib
Version: 1.1.14
Summary: Python Modules for Next-Generation Sequencing Data Analysis.
Home-page: http://tsznxx.appspot.com
Author: Yunfei Wang
Author-email: yfwang0405@gmail.com
License: GNU General Public License (GPL)
Description: =================
        Python-fontconfig
        =================
        
        Python bindings for ngslib_ library
        
        Requirement
        -----------
        
        - numpy_ scientific computation
        - pysam_ (>0.8.2) SAM/BAM file manipulation
        - argparse_ (required if Python2.6 is used)
        
        .. _numpy: http://www.numpy.org/
        .. _pysam: http://pysam.readthedocs.org/en/latest/
        .. _argparse: http://pymotw.com/2/argparse/
        
        
        
        
        Tested on
        ~~~~~~~~
        
        - ``Python 2.6.*`` (64-bit)
        - ``Python 2.7.*`` (64-bit)
        - ``CentOS 6.4``
        - ``Fedora 17``
        - ``RedHat 5.5``
        - ``Ubuntu 12.04`` (``python-dev`` and ``libpng-dev`` are required)
        
        
        Installation
        ------------
        
        From PyPI::
        
          >>> pip install ngslib
        
          or
        
          >>> easy_install ngslib
        
        From source::
        
          >>> easy_install --editable  --build-directory . ngslib
          >>> cd ngslib
          >>> python setup.py install
        
        
        Major modules
        -------------
        
        - **IO**: Read various biological data
        - **DB**: Build DB for genomic data for fast query.
        - **Pipeline**: Pipelines built using wrappers of commonly used tools.
        - **Bed**: Genomic coordinates data format.
        - **BedList**: A list of Bed instances.
        - **TwoBitFile**: python module for retrieve fasta sequence from 2bit file.
        - **BigWigFile**: python module for retrieve Wiggle region from BigWig file.
        - **mFile**: uniform interface for input types including regular file, sys.stdin/stdout and StringFile.
        
        
        Usage
        -----
        
        >>> import ngslib
        >>> for tbed in ngslib.IO.BioReader('test.bed','bed'):
                print tbed
        
        >>> bwf = ngslib.DB('test.bw','bigwig')
        >>> for wig in bwf.fetch('chr1',1000,2000):
                print wig
        >>> depth = bwf.pileup('chr1',3000,4000)
        >>> bwf.close()
        
        
        License
        -------
        
        This program is released under ``GPLv3`` license, see ``LICENSE`` for more detail.
        
Keywords: Python Sequencing Bed BigWig TwoBit
Platform: UNKNOWN
Classifier: Environment :: Console
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: GNU General Public License (GPL)
Classifier: License :: Free for non-commercial use
Classifier: Operating System :: Unix
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics