loop extrusion example

[SorenKyhl]

I've tried to get the examples/loopExtrusion/extrusion_3D.ipynb example going, but I've run into an error. The jupyter notebook tries to read in LEF positions from a "trajectory" directory that doesn't seem to exist. Is this example up to date?

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FileNotFoundError Traceback (most recent call last) Cell In[2], line 6 1 # -------defining parameters---------- 2 # -- basic loop extrusion parameters 4 folder = "trajectory" ----> 6 myfile = h5py.File("trajectory/LEFPositions.h5", mode='r')

FileNotFoundError: [Errno 2] Unable to open file (unable to open file: name = 'trajectory/LEFPositions.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

[henrik-dahl-pinholt]

I think this problem arises because the extrusion_3D code can only be run after first running a 1D loop extusion simulation.

Try to:

• First run extrusion_1D_newCode.ipynb. This should make the file you need.
• Then run this again.