{ "info": { "author": "Florian Aldehoff", "author_email": "f.aldehoff@student.uni-tuebingen.de", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "Environment :: X11 Applications :: Qt", "Intended Audience :: Science/Research", "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", "Natural Language :: English", "Operating System :: POSIX", "Programming Language :: Python :: 3 :: Only", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "=========\nSamSifter\n=========\n\nSamSifter helps you create filter workflows for next-generation sequencing\ndata. It is primarily used to process SAM files generated by MALT prior to\nmetagenomic analysis in MEGAN.\n\nQuick Start\n===========\n\nInstalling SamSifter\n--------------------\n\nInstalling or updating SamSifter is easy once you have a working Python3\nenvironment with ``PyQt4``, ``matplotlib``, ``numpy`` and ``pandas``. See the\n`Detailled Installation Instructions `_\nfor help on installing these required packages.\n\nDownload and install the current SamSifter package on your system by executing\nthe following command as administrator::\n\n\tpip3 install SamSifter\n\nPrevious versions will be uninstalled automatically. The installation can be\ntested with ::\n\n\tsamsifter --help\n\nIf everything went fine you should see the following help text::\n\n\tusage: samsifter [-h] [-v] [-d]\n\n\tSamSifter helps you create filter workflows for next-generation sequencing\n\tdata. It is primarily used to process SAM files generated by MALT prior to\n\tmetagenomic analysis in MEGAN.\n\n\toptional arguments:\n\t -h, --help show this help message and exit\n\t -v, --verbose print additional information to stderr\n\t -d, --debug show debug options in menu\n\nStarting the program without any arguments will display the GUI and let you\nedit your first workflow.\n\nFirst Steps\n-----------\n\nTo start working add filters to the empty workflow. You can add filters by\ndoubleclicking available entries in the righthand dock or by selecting an entry\nfrom the menu **[Edit > Add Filter...]**. Similarly, you can doubleclick filters\nin the workflow to edit their settings and parameters. The lefthand toolbar is\nused to move and delete filter steps.\n\nYou can save your workflow to a file, execute it right now by clicking the\n**[Run]** button and even export it to a Bash script to run it on another\nworkstation. Any errors and messages will be reported to you in the message dock\nat the bottom of the window.\n\nFeel free to re-arrange these docks to make yourself comfortable - SamSifter\nwill remember your settings. Accidentally closed docks can always be re-opened\nfrom the menu **[View]**.\n\nUninstalling SamSifter\n----------------------\n\nTo get rid of SamSifter simply execute the following command as administrator::\n\n\tpip3 uninstall SamSifter\n\nThe Python utility ``pip3`` will list all currently installed\navailable versions for selective removal. 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