Cool.fetch_data problem

[aminakur]

Hello, I am trying to plot a decay curve using the example from the documentation: https://gangcaolab.github.io/CoolBox/_gallery/decay.html

My code:

#Plot a decay curve of chr9:
import matplotlib.pyplot as plt
plt.rcParams['font.size'] = 18

cool_file = "/scratch/ak8725/az_mrg/az_mrg.mcool"
cool = Cool(cool_file, balance=False)

gr1 = "chr9:4000000-5000000"
gr2 = "chr9:5000000-6000000"

mat1 = Cool.fetch_data(gr1,gr2) # any genome region
decay1 = Cool.diagonal_mean(mat1)
mat2 = Cool.fetch_data(gr2)
decay2 = Cool.diagonal_mean(mat2)

binsize = cool.fetched_binsize

# plot
fig, ax = plt.subplots(figsize=(10, 5))
ax.plot(decay1, label=gr1)
#ax.plot(decay2, label=gr2)
plt.yscale('log')  # log scale on y-axis
plt.xlabel(f"Distance(bins, binsize={binsize})")
plt.ylabel("Mean contacts")
plt.xlim(0, 150)
plt.ylim(1e-1, 1e5)
plt.legend()

The error message:

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-28-cb0cc812cd10> in <module>
      9 gr2 = "chr9:5000000-6000000"
     10 
---> 11 mat1 = Cool.fetch_data(gr1,gr2) # any genome region
     12 decay1 = Cool.diagonal_mean(mat1)
     13 mat2 = Cool.fetch_data(gr2)

/opt/conda/lib/python3.8/site-packages/coolbox-0.3.8-py3.8.egg/coolbox/core/track/hicmat/cool.py in fetch_data(self, gr, **kwargs)
     38         from coolbox.utilities.hic.wrap import CoolerWrap
     39 
---> 40         path = self.properties['file']
     41         binsize = kwargs.get('resolution', self.properties.get('resolution', 'auto'))
     42         wrap = CoolerWrap(path, balance=self.balance, binsize=binsize)

AttributeError: 'str' object has no attribute 'properties'

What is the issue?

[zhqu1148980644]

Fix this line: Cool -> cool

mat1 = cool.fetch_data(gr1,gr2) # any genome region

[aminakur]

Thank you!