Metadata-Version: 1.1
Name: SamSifter
Version: 0.5.5
Summary: Workflow editor for metagenomic analysis
Home-page: http://pypi.python.org/pypi/SamSifter/
Author: Florian Aldehoff
Author-email: f.aldehoff@student.uni-tuebingen.de
License: LICENSE.txt
Description: =========
        SamSifter
        =========
        
        SamSifter helps you create filter workflows for next-generation sequencing
        data. It is primarily used to process SAM files generated by MALT prior to
        metagenomic analysis in MEGAN.
        
        Quick Start
        ===========
        
        Installing SamSifter
        --------------------
        
        Installing or updating SamSifter is easy once you have a working Python3
        environment with ``PyQt4``, ``matplotlib``, ``numpy`` and ``pandas``. See the
        `Detailled Installation Instructions <http://www.biohazardous.de/samsifter/docs/manual.html#installation>`_
        for help on installing these required packages.
        
        Download and install the current SamSifter package on your system by executing
        the following command as administrator::
        
        	pip3 install SamSifter
        
        Previous versions will be uninstalled automatically. The installation can be
        tested with ::
        
        	samsifter --help
        
        If everything went fine you should see the following help text::
        
        	usage: samsifter [-h] [-v] [-d]
        
        	SamSifter helps you create filter workflows for next-generation sequencing
        	data. It is primarily used to process SAM files generated by MALT prior to
        	metagenomic analysis in MEGAN.
        
        	optional arguments:
        	  -h, --help     show this help message and exit
        	  -v, --verbose  print additional information to stderr
        	  -d, --debug    show debug options in menu
        
        Starting the program without any arguments will display the GUI and let you
        edit your first workflow.
        
        First Steps
        -----------
        
        To start working add filters to the empty workflow. You can add filters by
        doubleclicking available entries in the righthand dock or by selecting an entry
        from the menu **[Edit > Add Filter...]**. Similarly, you can doubleclick filters
        in the workflow to edit their settings and parameters. The lefthand toolbar is
        used to move and delete filter steps.
        
        You can save your workflow to a file, execute it right now by clicking the
        **[Run]** button and even export it to a Bash script to run it on another
        workstation. Any errors and messages will be reported to you in the message dock
        at the bottom of the window.
        
        Feel free to re-arrange these docks to make yourself comfortable - SamSifter
        will remember your settings. Accidentally closed docks can always be re-opened
        from the menu **[View]**.
        
        Uninstalling SamSifter
        ----------------------
        
        To get rid of SamSifter simply execute the following command as administrator::
        
        	pip3 uninstall SamSifter
        
        The Python utility ``pip3`` will list all currently installed
        available versions for selective removal. Proceed similarly with any required
        packages (e.g. ``matplotlib``) if you don't need them anymore.
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: X11 Applications :: Qt
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Natural Language :: English
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
