No “weight” column after merging cooler files

[Jiangyuan-Liu]

I am trying to merge cooler files only for 5 and 10kb resolutions. However, the balancing “weight” column in the cooler bin-table disappeared after merging. Does anyone know how to solve this problem? Do I need to redo balancing to this merged mcool file?

Thanks,
Jiangyuan

for res in [10000, 5000]:
        merge_cool = '{}::/resolutions/{}'.format(Merge_cool,res)
        replicate_cool = ['{}::/resolutions/{}'.format(i,res) for i in input_files]
        print(merge_cool)
        cooler.merge_coolers(output_uri = merge_cool,
                             input_uris = replicate_cool,
                             mergebuf = int(20e6),
                             mode="a")
c1 = cooler.Cooler(Merge_cool+'::resolutions/10000')
c2 = cooler.Cooler(Merge_cool+'::resolutions/5000')

c2.bins()[:10] # No weight column
c3 = cooler.Cooler(input_files[0]+'::resolutions/10000')
c3.bins()[:10] # has weight column

[nvictus]

There is no prescribed way to "merge" the weights from different coolers. That's why it doesn't appear in the output.

Do I need to redo balancing to this merged mcool file?

Yes.

[Jiangyuan-Liu]

I got the following error when I redo balancing using cooler.balance_cooler(). I also tried hictk balance ice and got the following error. Did I merge these cooler files in a wrong way to generate an invalid merged mcool file? Thanks.

for res in [10000, 5000]:
    merge_cool = '{}::resolutions/{}'.format(Merge_cool,res)
    cooler.balance_cooler(merge_cool, store=True)

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
/tmp/ipykernel_1129194/1822552934.py in <module>
      1 for res in [10000, 5000]:
      2     merge_cool = '{}::resolutions/{}'.format(Merge_cool,res)
----> 3     cooler.balance_cooler(merge_cool, store=True)

~/miniconda3/envs/genomeinfodb-manual-versions2/lib/python3.8/site-packages/cooler/balance.py in balance_cooler(clr, cis_only, trans_only, ignore_diags, mad_max, min_nnz, min_count, blacklist, rescale_marginals, x0, tol, max_iters, chunksize, map, use_lock, store, store_name)
    339     """
    340     # Divide the number of elements into non-overlapping chunks
--> 341     nnz = int(clr.info["nnz"])
    342     if chunksize is None:
    343         chunksize = nnz

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

hictk balance ice Merge_cool.mcool

input: ((Not a valid .hic file: Merge_cool.mcool) OR (Not a valid Cooler: Merge_cool.mcool)) OR (Not a valid multi-resolution cooler: Merge_cool.mcool)
Run with --help for more information.

[nvictus]

The input should be a Cooler object and not a path.

for res in [10000, 5000]:
    merge_cool = cooler.Cooler('{}::resolutions/{}'.format(Merge_cool,res))
    cooler.balance_cooler(merge_cool, store=True)