idr-v2.0.2/2.0.3 running error

[WeiSheng Zheng]

Hi, all

I'm a PhD student from TJU. I've run IDR v2.0.2 and idr v2.0.3 (https://github.com/kundajelab/idr) with test data and my ChIP-seq data. They all ended up with a same error:

/home/wszheng/.conda/envs/test_py3/bin/idr -s tests/data/peak1 tests/data/peak2

Traceback (most recent call last):

  File "/home/wszheng/.conda/envs/test_py3/bin/idr", line 4, in <module>

    __import__('pkg_resources').run_script('idr==2.0.3', 'idr')

  File "/home/wszheng/Install/Python-3.6.1/lib/python3.6/site-packages/pkg_resources/__init__.py", line 654, in run_script

    self.require(requires)[0].run_script(script_name, ns)

  File "/home/wszheng/Install/Python-3.6.1/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1434, in run_script

    exec(code, namespace, namespace)

  File "/home/wszheng/Install/Source_binaries/idr-2.0.4/idr.egg-info/scripts/idr", line 10, in <module>

    idr.idr.main()

  File "/home/wszheng/Install/Source_binaries/idr-2.0.4/idr/idr.py", line 866, in main

    fix_mu=args.fix_mu, fix_sigma=args.fix_sigma )    

  File "/home/wszheng/Install/Source_binaries/idr-2.0.4/idr/idr.py", line 446, in fit_model_and_calc_local_idr

    fix_mu=fix_mu, fix_sigma=fix_sigma)

  File "/home/wszheng/Install/Source_binaries/idr-2.0.4/idr/optimization.py", line 468, in estimate_model_params

    fix_mu=fix_mu, fix_sigma=fix_sigma)

  File "/home/wszheng/Install/Source_binaries/idr-2.0.4/idr/optimization.py", line 420, in EMP_with_pseudo_value_algorithm

    z1 = compute_pseudo_values(r1, theta[0], theta[1], theta[3])

  File "/home/wszheng/Install/Source_binaries/idr-2.0.4/idr/utility.py", line 46, in py_compute_pseudo_values

    -10, 10, EPS ) )

I check the function py_cdf_i() in utility.py, this function takes 6 parameters in the definition(def py_cdf_i(r, mu, sigma, pi, lb, ub)), but in the calling action, it has 7 parameters (pseudo_values.append( cdf_i( new_x, signal_mu, signal_sd, p, -10, 10, EPS ) )). As I don't know what exactly these parameters mean, I can't solve this problem. Could you tell me how to solve this running error? 

Thanks very much

--wszheng

[Jin]

Did you have cython installed on your system? If so the following command should work.

python -c "from Cython.Compiler.Version import version; print version"

Jin

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