Mixed usage of Python2 and Python3.

[aakashsur]

It looks like s4_bin.sh uses python (which maps to python2 usually) instead of python3. I'm assuming they can all be run using python3 so I guess I would either change the python calls in the bash script or update the documentation to reflect the Python 2 usage before that step.

[yezhengSTAT]

All the python scripts in mHi-C are tested using python3.

[aakashsur]

Okay, then it looks like changing these lines should fix the problem:

mHiC/s4_bin.sh

Lines 166 to 173 in 0d34bee

	if [ "$normMethod" != "None" ] && [ "$normMethod" != "NONE" ] && [ "$normMethod" != "none" ] && [ "$normMethod" != "" ]; then
	if [ "$normMethod" == "ICE" ] || [ "$normMethod" == "ice" ]; then
	# ICE normalization with filtering low mappability regions
	python $bin/ICE-with-sparseMatrix.py $validI.binPairCount.uni.minCount$minCount $mappFile l1 $validI.binPairCount.uni.ICEnorm $minMap $maxIter
	else
	python $bin/KR_norm_mHiC.py -r $resolution -l $chromSizeFile -c "whole" -tr $sparsePerc -f $validI.binPairCount.uni.minCount$minCount -o $dir
	fi

[yezhengSTAT]

Thanks.