ImportError: cannot import name expm3

Question

[taniamahmood38]

Dear all,

I am trying to use pool-HMM tool on my pooled-seq data. It requires python version < 3 and I have python2.7. But the module SciPy was missing. So, i tried to install it with command:

pip2 install scipy

Now, whenever i try to run my pool-HMM command it gives error:

 Traceback (most recent call last):
  File "pool-hmm.py", line 20, in <module>
    from pred import prediction
  File "/media/tania/TM/WG_pooled_seq_analysis/PoolHMM-master/Modules/pred.py", line 2, in <module>
    from scipy.linalg import expm3
ImportError: cannot import name expm3

Please help me out how to resolve this issue? Any help would be highly appreciated.

Thanks in advance

Answer 1

[Mensur Dlakic]

Part of the answer to your question is here. Briefly, expm3 function was removed from scipy a long time ago, which tells me that the script you are using is very old as it relies on ancient functions. Maybe forcing the installation of an old scipy release will work, but beware that it will probably lack functionality that more recent scripts may need.

pip2 install scipy==0.12.1

[taniamahmood38]

I am really grateful to you. It worked, many thanks for your help.