The repository contains base code for Python integration with the Epiviz tool. It also contains a demo that exemplifies usage and potential extension.

A different demo with real world data can be found in the demo branch

(Optional) Open project using Eclipse PyDev

• Python 2.7
• pip install simplejson
• pip install tornado
• pip install enum
• (For the demo branch: pip install pandas)

Launch main.py

Open Epiviz to visualize the data: http://epiviz.cbcb.umd.edu/?websocket-host[]=ws://localhost:8888/ws&settings=default&

Type the following commands in the command line to see the demo at work:

addMeasurements will add a mock measurement to Epiviz. You can type this command several times, and each time a new measurement will be added. (The measurements have the Default chart set to Line Track and they are prefixed with Python Measurement.)

removeMeasurements will remove the last mock measurement added. If no measurement has been added through EpivizPy, nothing will happen.

addChart once at least one measurement has been added through EpivizPy, this command will add a new Line Track to the workspace, showing that measurement.

removeChart removes the last chart added using EpivizPy

getCurrentLocation queries Epiviz for the current genomic location of the workspace.

navigate can only be called after calling getCurrentLocation. Causes Epiviz to navigate right.

redraw causes Epiviz to redraw all charts.

On Windows, when running pip install pandas, you get the following error:

Command "C:\Python27\python.exe -c "import setuptools, tokenize;_file__='c:\\users\\mms\\appdata\\local\\temp\\pip-build-v8ycdd\\numpy\\setup.py';exec(compile(getattr(tokenize, 'open', open)(__file_).read().replace('\r\n', '\n'), _file_, 'exec'))" install --record c:\users\mms\appdata\local\temp\pip-n35ir4-record\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in c:\users\mms\appdata\local\temp\pip-build-v8ycdd\numpy

This is a known problem with Python in Windows. The solution, as outlined in this post is:

1. Make sure you are running Python 2.7 (32 Bit version)
2. Install visual c++ 2008: http://go.microsoft.com/?linkid=7729279 (pip needs the C++ compiler from this version of Visual Studio; newer versions will not work!)
3. Now for the even more annoying part: open regedit (Windows Start button > type regedit ); find the following key path: HKEY_LOCAL_MACHINE\Software\Wow6432Node\Microsoft\VisualStudio\9.0\Setup\VC (on a 64 bit Windows). If any of those keys does not exist, create them.
4. Right-click on the VC key, and select New > String value. The name should be ProductDir, and the value, the directory location of vcvarsall.bat (for example: c:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\).
5. Open command prompt with administrator privileges, go to c:\Python27\Scripts (or your corresponding location of the Python 2.7 installation).
6. Run C:\Python27\Scripts>pip install --upgrade pip. Don't worry if this looks like it fails. Then try pip install pandas again. This may take a long time but should not fail this time.