Metadata-Version: 1.1
Name: wormtable
Version: 0.1.0a1
Summary: Write-once read-many data sets using Berkeley DB.
Home-page: http://pypi.python.org/pypi/wormtable
Author: Jerome Kelleher, Dan Halligan, Rob Ness
Author-email: jerome.kelleher@ed.ac.uk
License: GNU GPLv3
Description: ===============================================
        Wormtable
        ===============================================
        
        Wormtable is a write-once read-many table for large scale datasets.
        It provides Python programmers with a simple and efficient method of 
        storing, processing and searching datasets of essentially unlimited
        size. A wormtable consists of a set of rows, each of which contains 
        values belonging to a fixed number of columns. Rows are encoded 
        in a custom binary format, designed to be flexible, compact and 
        portable. These rows are then stored on disc using Berkeley DB,
        a highly respected embedded database toolkit. Wormtable also 
        supports efficient searching and retrieval of rows with particular
        values through the use of indexes.
        
        The Variant Call Format (VCF) is supported directly by wormtable
        through a command line conversion program, vcf2wt. There is also a
        command line utility wtadmin to manage wormtables, including the ability to 
        dump values and add, remove and view indexes.
        
        -------------
        Documentation
        -------------
        
        Here's a quick example for the impatient::
        
                import wormtable as wt 
                with wt.open_table("example.wt") as t:
        	    c = t.cursor("POS", "ALT", "REF")
        	    for pos, alt, ref in c:
        	    	print(pos, ":", alt, ":", ref)
        
        Full documentation for ``wormtable`` is available at `<http://jeromekelleher.github.com/wormtable>`_.
        
        ------------
        Installation
        ------------
        
        Wormtable requires Berkeley DB, which is available for all major platforms.  
        Any recent version of Berkeley DB should work, but the various versions 
        have not been tested extensively. Development and testing have been 
        carried out primarily on the DB 4.x series.
        
        Once DB has been installed (see below) we can build the ``wormtable`` module using the 
        standard Python `methods <http://docs.python.org/install/index.html>`_. For 
        example, using pip we have ::
                
                $ sudo pip install wormtable
        
        Or, we can manually download the package, unpack it and then run::
                
                $ python setup.py build
                $ sudo python setup.py install
        
        Most of the time this will compile and install the module without difficulty.
        
        It is also possible to download the latest development version of 
        ``wormtable`` from `github <https://github.com/jeromekelleher/wormtable>`_. 
        
        ----------------------
        Installing Berkeley DB
        ----------------------
        
        *****
        Linux
        *****
        Wormtable is primarily developed on Linux and should work very well on any 
        modern Linux distribution. Installing Berkeley DB is very easy on Linux 
        distributions. 
        
        On Debian/Ubuntu use::
        
                $ sudo apt-get install libdb-dev 
        
        and on Red Hat/Fedora use::
        
                # yum install db4-devel
        
        Other distributions and package managers should provide a similarly easy
        option to install the DB development files.
        
        ********
        Mac OS X
        ********
        
        TODO: document installation on a mac. MacPorts/Homebrew/installer package?
        
        *****
        Unix
        *****
        
        Most Unix systems provide Berkeley DB packages. For example, on FreeBSD
        we have::
        
            # pkg_add -r db48
        
        If necessary, Berkeley DB can be built from source and installed manually quite 
        easily.
        
        ******************
        Potential problems
        ******************
        
        On platforms that Berkeley DB is not available as part of the native packaging 
        system (or DB was installed locally because of non-root access)
        there can be issues with finding the correct headers and libraries
        when compiling ``wormtable``. For example, on FreeBSD we get something 
        like this::
        
                $ python setup.py build
                ... [Messages cut for brevity] ...
                _wormtablemodule.c:3727: error: 'DB_NEXT_NODUP' undeclared (first use in this function)
                _wormtablemodule.c:3733: error: 'DB_NOTFOUND' undeclared (first use in this function)
                _wormtablemodule.c:3739: error: 'DistinctValueIterator' has no member named 'cursor'
                _wormtablemodule.c:3739: error: 'DistinctValueIterator' has no member named 'cursor'
                _wormtablemodule.c:3740: error: 'DistinctValueIterator' has no member named 'cursor'
                error: command 'cc' failed with exit status 1
        
        To remedy this we must set the 
        ``LDFLAGS`` and ``CFLAGS`` environment variables to 
        their correct values. Unfortunately there is no simple method to do this 
        and some knowledge of where your system keeps headers and libraries 
        is needed.  On FreeBSD (after installing the ``db48`` package as above) we 
        might use::
                
                 $ CFLAGS=-I/usr/local/include/db48 LDFLAGS=-L/usr/local/lib/db48 python setup.py build
        
        ----------
        Test suite
        ----------
        
        Wormtable has an extensive suite of tests to ensure that data
        is stored correctly.
        It is a good idea to run these immediately after installation::
        
                $ python tests.py
        
        
        ****************
        Tested platforms
        ****************
        
        Wormtable is higly portable, and 
        has been successfully built and tested 
        on the following platforms:
        
        ================        ========        ======          ===========     
        Operating system        Platform        Python          Compiler        
        ================        ========        ======          ===========     
        Ubuntu 13.04            x86-64          2.7.4           gcc 4.7.3       
        Ubuntu 13.04            x86-64          3.3.1           gcc 4.7.3       
        Ubuntu 13.04            x86-64          2.7.4           clang 3.2.1     
        Debian squeeze          x86-64          2.6.6           gcc 4.4.5       
        Debian squeeze          x86-64          3.1.3           gcc 4.4.5        
        Debian squeeze          x86-64          3.1.3           clang 1.1 
        Debian squeeze          ppc64           2.6.6           gcc 4.4.5	    
        Debian squeeze          ppc64           3.1.3           gcc 4.4.5	
        Debian squeeze          ppc64           3.1.3           clang 1.1 
        Debian wheezy           armv6l          2.7.3           gcc 4.6.3
        Fedora 17               i386            2.7.3           gcc 4.7.2
        Fedora 17               i386            3.2.3           gcc 4.7.2
        FreeBSD 9.0             i386            3.2.2           gcc 4.2.2        
        FreeBSD 9.0             i386            2.7.2           gcc 4.2.2        
        FreeBSD 9.0             i386            3.1.4           clang 3.0 
        ================        ========        ======          ===========     
        
        
Keywords: Berkeley DB,VCF,Variant Call Format,Bioinformatics
Platform: POSIX
Classifier: Programming Language :: C
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Other Environment
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: POSIX
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires: argparse
