fastStructure can not import "allelefreq" module

[JingjingYang1226]

I had trouble in the using of  fastSTRUCTURE. The dependence of Numpy, Scipy, and Cython were installed by  pip of conda. GSL-2.3 were also installed successful, and the library was added to bash_profile.
 I had installed the fastSTRUCTURE step by step according to the instruction. However, when I typed pthon structure.py,  it appeared that fastStructure can not import "allelefreq" module.  I had checked the vars directory, it seemed that the "allelefreq" module were installed.
I don't known what's wrong.  I had provided the IMAGE in the attachment.

python structure.py

Traceback (most recent call last): File "structure.py", line 3, in import fastStructure File "fastStructure.pyx", line 2, in init fastStructure import numpy as np File "admixprop.pyx", line 1, in init admixprop ImportError: No module named allelefreq

Vars direcrory

admixprop.c allelefreq.c build init.pyc README admixprop.h allelefreq.h C_admixprop.c marglikehood.c setup.py admixprop.pxd allelefreq.pxd C_allelefreq.c marglikehood.h utils.c admixprop.pyx allelefreq.pyx C_marglikehood.c marglikehood.pyx utils.pyx admixprop.so allelefreq.so init.py marglikehood.so utils.so

[yaominzoe]

I am getting this as well when I try to run the testing dataset. Have you found a solution to this problem?

[yaominzoe]

wow，you could try this method: https://gist.github.com/josiahaltschuler/a063e03b4197013def53f9a0abc6dfed It works for me.

[dslater82]

I tried the method from https://gist.github.com/josiahaltschuler/a063e03b4197013def53f9a0abc6dfed but I still receive "ImportError: No module named allelefreq". I am using Python 2.7.13 with numpy 1.16.5, scipy 0.19.0, and 0.29.14. Any ideas?

[jawzman7]

I am getting the same issue...no module named allelefreq...Did anyone figure it out?????

[VarIr]

Following the guide works for me. I created a virtualenv to ensure the exact package versions stated in the guide. Do you have GSL installed and did you set LD_LIBRARY_PATH, CFLAGS, and LDFLAGS according to the guide (adapted for your individual paths)?

[camhilker]

I'm having the same issue. I updated my bash profile and compiled the cython scripts as outlined in the README file. Any help is appreciated! I'm using python 2.7, numpy 1.16.6, scipy 1.2.1, cython 0.29.14.

[jawzman7]

I got it to work when I created a python environment to work in

[jawzman7]

a python virtual environment like Varlr suggested.

[Nguyen205]

I solved this problem by editing the three paths (LD_LIBRARY_PATH, CFLAGS, and LDFLAGS) in .bashrc. Note that the CFLAGS path was slightly different from the methods above. It should be the path containing the .h files. Mine was: xxx/gsl/include/gsl rather than xxx/gsl/include. The other two paths should be the path containing the .so files, which was the same as the methods provided by other people. After doing that, I deleted the entire proj folder and redid the installation following the readme file. After all these steps, it worked for me.

[StuntsPT]

Hi everyone, I have a stop-gap solution if you are on a GNU/Linux based or macOS platform. I am the developer of Structure_threader, which contains a pre-compiled fastStructure binary for both mentioned platforms. You can either install Structure_threader using pip (python3 -m pip install structure_threader --user), or you can get the binary file directly here for GNU/Linux, or here for macOS X (not tested on the latest ARM based macs, though).

Of course the only real solution to this issue is porting fastStructure to python3... but I do hope this helps, though.