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"description": "perseuspy README\n================\n\n.. image:: https://readthedocs.org/projects/perseuspy/badge/?version=latest\n :target: http://perseuspy.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation Status\n\n.. sphinx-inclusion-marker-do-not-remove\n\n.. image:: https://travis-ci.org/jdrudolph/perseuspy.svg?branch=master\n :target: https://travis-ci.org/jdrudolph/perseuspy\n\nUtility and covenience functions for Python-Perseus interop.\nBuilding on the `pandas` package. If you intend to develop\na plugin for Perseus, please see `PluginInterop `_.\n\nInstallation (short)\n--------------------\n\n.. code:: bash\n\n pip install perseuspy\n\nUpdating to the latest version\n------------------------------\n\n.. code:: bash\n\n pip install --upgrade perseuspy\n\nInstallation (Windows long)\n---------------------------\nFirst open a terminal by searching for `cmd.exe` in the start menu. Here we can easily\ncheck if all required programs are installed.\n\n#. Check to see if the `pip` executable is already available.\n ::\n\n pip install perseuspy\n\n If there is no error you are already done. If it fails, continue with the next steps.\n#. Navigate to the installation directory of your `Python` installation. If it is installed\n e.g. `D:/Programs/Python/` we would first change the drive letter (maybe unnecessary)\n and then go to the installation directory.\n ::\n\n D:\n cd Programs/Python\n\n Now we should be able to run `python` from the command line.\n ::\n \n python.exe --version\n\n This should print the installed version of python\n#. Navigate to the `Scripts` directory and run the installation\n ::\n\n cd Scripts\n pip install perseuspy\n\n If you want to upgrade you installation, run\n ::\n\n pip install --upgrade perseuspy\n\n#. Test the installation by navigating back to the `Python` folder and trying to import `perseuspy`.\n ::\n\n cd ..\n python.exe\n\n Now you should be inside the `python` interpreter. Check the installation by running.\n ::\n\n import perseuspy\n\n If the command doesn't produce any error you can exit `python` by pressing `CTRL+c`.\n#. Add `python` to your `PATH` (optional). Makes it easier for Perseus to find the Python\n installation. There are many resources on how to add programs to the `PATH` available online.\n\nUsage\n------------\nYou can use `perseuspy` just like any other python module.\n\n\n.. code:: python\n\n # import a monkey-patched version of pandas\n from perseuspy import pd\n df = pd.read_perseus('matrix1.txt')\n df2 = df.dropna()\n df2.to_perseus('matrix2.txt')\n\n\nPlugin template\n---------------\nThe following snippet can be used as a starting point\nfor python scripting in Perseus.\n\n.. code:: python\n\n import sys\n from perseuspy import pd\n from perseuspy.parameters import *\n _, paramfile, infile, outfile = sys.argv # read arguments from the command line\n parameters = parse_parameters(paramfile) # parse the parameters file\n df = pd.read_perseus(infile) # read the input matrix into a pandas.DataFrame\n some_value = doubleParam(parameters, 'some value') # extract a parameter value\n df2 = some_value / df.drop('Name', 1)\n df2.to_perseus(outfile) # write pandas.DataFrame in Perseus txt format\n \nNetwork Plugin template\n-----------------------\nThe following snippet can be used as a starting point\nfor python scripting in Perseus (for networks).\n\n.. code:: python\n\n import sys\n from perseuspy import nx, pd, read_networks, write_networks\n _, paramfile, infolder, outfolder = sys.argv # read arguments from the command line\n networks_table, networks = read_networks(infolder) # networks in tabular form\n graphs = nx.from_perseus(networks_table, networks) # graphs as networkx objects\n _networks_table, _networks = nx.to_perseus(graphs) # convert back into tabular form\n write_networks(tmp_dir, networks_table, networks) # write to folder\n\n\nGenerating the documentation\n----------------------------\nRun `./generate_docs.sh` from `bash`.\n\nLicensing and Contributions\n---------------------------\n`perseuspy` is licensed under the MIT lisence.\nContributions are welcome! If you are interested in contributing to code or documentation,\nplease read `CONTRIBUTING.rst `_.",
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