Assemble self.N50 Error

francicco commented 5 years ago

Hi,

I'm running assemble using this command line:

assemble -m hic_corrected.h5 -o ./assembly_output \
                --min_scaffold_length 100000 --bin_size 5000 --misassembly_zscore_threshold -1.0 \
                --num_iterations 3 --num_processors $THREADS

But I'm getting this

Traceback (most recent call last):
  File "/home/fc464/software/hicexplorer/bin/assemble", line 11, in <module>
    import hicassembler.HiCAssembler as HiCAssembler
  File "/home/fc464/software/hicexplorer/lib/python3.6/site-packages/hicassembler/HiCAssembler.py", line 226
    print self.N50
             ^
SyntaxError: Missing parentheses in call to 'print'

Anyway I could fix this? Thanks F

francicco commented 5 years ago

Apparently

HiCExplorer does no longer support Python 2. This dependency issue needs to be solved by HiCAssembler

Need to find another HiC assembler...

xinl22 commented 5 years ago

@francicco Hi, have you fixed this issue?

fidelram commented 5 years ago

I had made some progress with a python3 version of hicassembler. The code is in the https://github.com/maxplanck-ie/HiCAssembler/tree/2to3 branch for those who wants to try it.

I still see some errors in the doctests that need to be investigated.

maxplanck-ie / HiCAssembler

Assemble self.N50 Error #14