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deeptools / HiCExplorer

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
https://hicexplorer.readthedocs.org
GNU General Public License v3.0
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cool to h5 convert #429

Closed jiadong324 closed 5 years ago

jiadong324 commented 5 years ago

I am using the command (below) to convert cool format to h5, so that I can use hicMatrixPlot.

hicConvertFormat -m K562.50kb.cool -o K562.50kb --inputFormat cool --outputFormat h5

But it raises errors, which shows:

INFO:numexpr.utils:NumExpr defaulting to 4 threads. Traceback (most recent call last): File "/usr/local/bin/hicConvertFormat", line 7, in <module> main() File "/usr/local/lib/python2.7/site-packages/hicexplorer/hicConvertFormat.py", line 162, in main pApplyCorrectionCoolerLoad=applyCorrectionCoolerLoad) File "/usr/local/lib/python2.7/site-packages/hicmatrix/lib/matrixFileHandler.py", line 20, in __init__ self.matrixFile = self.class_(pMatrixFile) File "/usr/local/lib/python2.7/site-packages/hicmatrix/lib/cool.py", line 26, in __init__ super().__init__(pMatrixFile) TypeError: super() takes at least 1 argument (0 given)

Please help and thanks!

joachimwolff commented 5 years ago

Hi,

You do not need to convert cool to h5, HiCExplorer supports cool natively.

However, you get this error because you run HiCExplorer with Python 2.7 which is not supported by us. Please upgrade to Python 3.6.

Best,

Joachim

jiadong324 commented 5 years ago

Thanks, I will upgrade my python version and use cool format directly.