Weight column missing

[ratheraarif]

HI,
I need to run the following code from cooltools

# cvd == contacts-vs-distance cvd = cooltools.expected_cis( clr=clr, view_df=hg38_arms, smooth=False, aggregate_smoothed=False, nproc=4 #if you do not have multiple cores available, set to 1 )

However it flags the error cooler is not balanced, or balancing weight weight is not available in the cooler
Note that I generated the mcool files from .hic data using the following code hic2cool convert file1.allValidPairs.hic file2 -r 0 , which probably misses the weight column. I can balance the matrix through cooler.balance_cooler(clr), however, I cannot add it to the bins.

Please help me to fix this issue

[Phlya]

https://cooltools.readthedocs.io/en/latest/cooltools.html#cooltools.api.expected.expected_cis
This function has a clr_weight_name argument, with coolers produced from .hic files specify an existing weight, e.g. clr_weight_name='KR' and it should work.
Same should apply to all functions in cooltools.

[ratheraarif]

I did the same but it still generates the error..

[Phlya]

Right, ok. Then just use cooler balance command in the terminal, that's the easiest way to balance probably.

[ratheraarif]

Thank you for your reply,

I can see that I can create a balancing using cooler balance ,but this lets me balance each resolution separately. Is there a way to balance the entire mcool file simultaneously, irrespective of the number of resolutions..
Please help with the code example

[Phlya]

No, just run cooler balance for each resolution.
Here is a bash one-liner for that:

for i in `cooler ls <file.mcool>`;  do cooler balance $i; done;