Python 3

[dominik-handler]

Hi, I saw that you have the branch 2to3 to migrate HiCAssembler to python 3. As it is getting quite difficult to install all dependencies for python 2.7 I wanted to try this branch. First of all I ran into an issue while installing this version: error in HiS Assembler setup command: "values of 'package_data' dict" must be a list of strings (got '*.txt')

Also, before I invest time in testing HiCAssembler in python 3, is it fully functional yet?

All the best and thank you, Dominik

[xuzhougeng]

I solve this problem by the following step

git clone https://github.com/maxplanck-ie/HiCAssembler.git
cd HiCAssembler/
git branch 2to3

and I edit the setup.py, and commment the the following line

#package_data={'': '*.txt'},

then I install this package locally

cd ..
pip install ./HiCAssembler/

[EarlyEvol]

xuzhougeng's fix resolves the first issue (same as dominik) but a new python 2>3 version issue remains:

Traceback (most recent call last):
  File "/home/u14/earlm1/miniconda3/envs/hic/bin/assemble", line 11, in <module>
    import hicassembler.HiCAssembler as HiCAssembler
  File "/home/u14/earlm1/miniconda3/envs/hic/lib/python3.6/site-packages/hicassembler/HiCAssembler.py", line 226
    print self.N50
             ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print(self.N50)?

xuzhougeng, Did you encounter the same error, or do I have a problem pulling the correct version of HiCAssembler.py? I started from a clean miniconda3 env, installed HiCExplorer, then did your 2to3 HicAssembler install instructions.

Earl

[EarlyEvol]

Ahh needed a different command to pull the correct branch: git checkout -b 2to3 --track origin/2to3 Don't understand git at all, but it worked.
(still needed the setup.py edit)

[yuzhenpeng]

I also get the same errors. could you please give me more help.

[yuzhenpeng]

It seems that import hicexplorer.HiCMatrix as HiCMatrix should be changed to import hicmatrix.HiCMatrix as HiCMatrix. #21