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open2c / coolpuppy

A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
MIT License
77 stars 11 forks source link

[Q]How to get the matrix data after running coolpup.py #141

Closed valderpan closed 6 months ago

valderpan commented 6 months ago

Hi, I ran the following command: coolpup.py WT_20000.iced.cool WT.mm10_allchr.20kb.TAD.bed --expected mm10_KO_expected_cis.tsv --rescale --local -p 10

I want to plot a plot like the one below : example_local_rescaled_pileup

After running this command I get a clpy file, when I try to check it I'm told it's a binary file that can't be viewed.

I want to customize the plot based on the generated file, even though the clpy can be plotted via plotpup.py

Can you tell me how to get the matrix file for the plot or is there any way to convert the clpy to an np.txtfile (like the txt file mentioned by paper)?

Phlya commented 6 months ago

Are you familiar with Python at least a little bit? Sorry about the format change, but now the files store a lot of metadata that is difficult to keep in a text file...

valderpan commented 6 months ago

Thank you for your quick reply. I don't know much about plotting with matplotlib, so I want to get the raw data to do it through R.

Phlya commented 6 months ago

Did you close the issue because you figured it out?