can't perform sequential mu.pp.filter_obs

[crichgriffin]

I want to perform multiple filtering steps on my object e.g.:

mu.pp.filter_obs(mdata, 'n_genes_by_counts', lambda x: (x >= 100))
mu.pp.filter_obs(mdata,  'total_counts', lambda x: (x >= 500) & (x <= 50000)

Error message:

muon/_core/preproc.py in filter_obs(data, var, func)
    733         # filter_obs() for each modality
    734         for m, mod in data.mod.items():
--> 735             obsmap = data.obsmap[m][obs_subset]
    736             obsmap = obsmap[obsmap != 0] - 1
    737             filter_obs(mod, mod.obs_names[obsmap])

anndata/_core/aligned_mapping.py in __getitem__(self, key)
    146 
    147     def __getitem__(self, key: str) -> V:
--> 148         return self._data[key]
    149 
    150     def __setitem__(self, key: str, value: V):

KeyError: 'x'

Minimal working example:

import numpy as np
import muon as mu
x = mu.AnnData(X=np.random.normal(size=1000).reshape(-1, 100))
y = mu.AnnData(X=np.random.normal(size=2000).reshape(-1, 100))

md = mu.MuData({"x": x, "y": y})

md['x'].obs['total_count'] = md['x'].X.sum(axis=1)
md['x'].obs['min_count'] = md['x'].X.min(axis=1)
md.update()

# filter one of the modalities.
mu.pp.filter_obs(md, 'x:min_count', lambda x: (x < -2))
mu.pp.filter_obs(md, 'x:total_count', lambda x: (x >0))

If you put md.update() between the two filter statements it does work. But to me this is not ideal if you are filtering on lots of categories sequentially

Is this desired behaviour ot something that could be updated such that one could just one run update command after sequential filters??

• OS: CentOS Linux release 7.8.2003 (Core)
• Python 3.9.5
• Versions of libraries involved
  • numpy 1.20.3
  • muon 0.1.1

Thanks!

[gtca]

Hey @crichgriffin, thanks for reporting, and thanks @ilia-kats for addressing it!
Should work now, and we've also added this scenario as a test.

[crichgriffin]

Great, thanks!