Metadata-Version: 1.1
Name: SamSifter
Version: 0.3.0
Summary: Workflow editor for metagenomic analysis
Home-page: http://www.biohazardous.de/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.
        
        Typical usage often looks like this::
        
            $ python3 samsifter
        
        .. image:: docs/screenshot_v0.1.0.png
        	:scale: 50%
        	:alt: Screenshot of SamSifter version 0.1.0
        	:align: center
        	:target: docs/screenshot_v0.1.0.png
        
        .. contents:: Contents
        
        Installation
        ============
        
        SamSifter is written in Python3, so you need a working Python3 interpreter.
        It requires the additional packages ``PyQt4`` to display the GUI, ``numpy``
        for vectorized calculations, ``pandas`` for statistical summaries, and
        ``matplotlib`` to plot
        optional coverage and read lengths distributions. The Python setup tools normally
        take care of these requirements for you, however at time of writing the package
        ``PyQt4`` is not available in the
        `PyPI repositories <http://https://pypi.python.org/pypi>`_ so you have to
        install it using your operating system's package management.
        
        If you already have a working Python3 installation with all required packages
        you can skip the following section.
        
        Installing ``Python3`` and ``PyQt4``
        ------------------------------------
        
        Below you can find tested installation instructions for Debian-based
        **GNU/Linux** distributions. The package names for other Linux distributions
        should be very similar though. The **Windows** installation has only been tested
        on a 32-bit Windows XP installation (currently the only test system available).
        The installation instructions for **Mac OS X** are likely incomplete as they
        could not be tested at all.
        
        Debian 8 (jessie) and newer or Ubuntu 14.04 and newer
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        The preparation of the SamSifter installation on Debian 8 (jessie)
        and newer or Ubuntu 14.04 and newer is very simple as all packages are already
        available in the standard repositories::
        
        	sudo aptitude install python3 python3-dev python3-setuptools python3-nose python3-pyqt4 python3-numpy python3-matplotlib python3-pandas
        
        You can now proceed with the actual SamSifter installation.
        
        Older Debian or Ubuntu systems
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        Older Debian/Ubuntu systems provide only a rudimentary Python3 environment
        lacking the ``matplotlib`` package. We have to use the Python tools
        ``easy_install`` and ``pip`` to obtain it. The following steps have been tested
        successfully on Ubuntu 12.04::
        
        	# install Python3 system (as far as possible)
        	sudo aptitude install python3 python3-dev python3-setuptools python3-nose python3-pyqt4 python3-numpy python3-tornado libfreetype6-dev
        	# install pip for Python3
        	sudo easy_install3 -U distribute
        	sudo easy_install3 pip
        	# matplotlib is not yet available, thus we install it from PyPI
        	sudo pip3 install matplotlib==1.3.1
        	# same for pandas
        	sudo pip3 install pandas==0.14.1
        
        You can now proceed with the actual SamSifter installation.
        
        Mac OS X using Homebrew
        ^^^^^^^^^^^^^^^^^^^^^^^
        
        Using `Homebrew <http://brew.sh>`_, the "missing package manager for OS X",
        seems to be the easiest way to obtain an up to date ``Python3`` system including
        ``PyQt4`` on a Mac. Install ``Homebrew`` by pasting the following command into a
        Terminal prompt::
        
        	ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
        
        and follow the on-screen instructions. Once you have checked that the system is
        functional with ::
        
        	brew doctor
        
        you can install these packages with the following commands (current versions at
        time of release according to `Braumeister <http://braumeister.org/search>`_)::
        
        	brew install python3        # current version: 3.4.2
        	brew install pyqt           # current version: 4.11.3
        	brew install pkg-config     # current version: 0.28
        
        Open a fresh Terminal window, confirm that it uses the newly installed Python3
        interpreter at `/usr/local/bin/python` by running ::
        
        	which python
        
        and continue to install additional Python packages with the built-in package
        management::
        
        	# install pip
        	easy_install -U distribute
        	easy_install pip
        	# install setuptools, numpy and matplotlib
        	pip install setuptools
        	pip install numpy
        	pip install matplotlib==1.3.1
        	pip install pandas==0.14.1
        
        You can now proceed with the actual SamSifter installation.
        
        Windows (32 bit)
        ^^^^^^^^^^^^^^^^
        
        For any Windows system the use of a packaged Python 3.4 distribution like ``Anaconda``
        from http://continuum.io/downloads#all is recommended. However, if you'd rather
        install the individual packages by yourself you can follow these steps.
        The following instructions have been tested successfully on Windows XP (32 bit):
        
        1. Download and install Python from https://www.python.org/downloads/windows/.
           The recommended version is
           `Python 3.4.2 <https://www.python.org/ftp/python/3.4.2/python-3.4.2.msi>`_.
           During installation, make sure to include ``pip`` in the installation and
           check the option to automatically add ``python.exe`` to your ``PATH``.
        
        2. Download and install ``PyQt4`` from
           http://www.riverbankcomputing.com/software/pyqt/download.
           The recommended version is
           `PyQt 4.11.3 for Python 3.4 and Qt 4.8.6 <http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-4.11.3/PyQt4-4.11.3-gpl-Py3.4-Qt4.8.6-x32.exe>`_.
        
        3. Download and install ``numpy`` from http://www.numpy.org/. The recommended
           version is
           `numpy 1.9.1 for Python 3.4 <http://downloads.sourceforge.net/project/numpy/NumPy/1.9.1/numpy-1.9.1-win32-superpack-python3.4.exe>`_.
        
        4. Download and install ``matplotlib`` from http://www.matplotlib.org/. The
           recommended version is `matplotlib 1.4.0 for Python 3.4  <http://downloads.sourceforge.net/project/matplotlib/matplotlib/matplotlib-1.4.0/matplotlib-1.4.0.win32-py3.4.exe>`_.
        
        5. Download and install ``pandas`` from
           http://www.lfd.uci.edu/~gohlke/pythonlibs/#pandas. The recommended version is
           ``pandas`` 0.15.2 for Python 3.4.
        
        You can now proceed with the actual SamSifter installation.
        
        Installing SamSifter
        --------------------
        
        Once you have a working Python3 environment unpack the SamSifter package::
        
        	cd /path/to/your/download/directory
        	tar -xf SamSifter-x.y.z.tar.gz
        	cd SamSifter-x.y.z/
        
        and install it either system-wide (as root or admin user)::
        
        	python3 setup.py install
        
        or locally::
        
        	python3 setup.py install --user
        
        After system-wide installation the SamSifter scripts are immediately available.
        In case of a local installation you may have to add the directory containing the
        scripts to your ``PATH`` variable. On Linux systems this is done with::
        
        	PYTHONPATH=$PYTHONPATH:~/.local/bin/
        	export PYTHONPATH
        
        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.
        
        Uninstalling SamSifter
        ----------------------
        
        To get rid of SamSifter simply execute the following command::
        
        	pip3 uninstall SamSifter
        
        for your local installation or::
        
        	sudo pip3 uninstall SamSifter
        
        for the systemwide installation. ``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
