scverse / scverse/scirpy

Can't save h5mu from Scirpy processed gex+bcr+tcr data if I copy airr into obs

Open
#434 3 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

bug
Dominant language
Python
Stars
265
Forks
50
Avg merge
9d 9h
Merged PRs (30d)
4

Description

Describe the bug

Can't save h5mu from Scirpy processed gex+bcr+tcr data if I copy airr into obs (i.e. tdata.obs = tdata.obs.join(ir.get.airr(tdata, tdata.obsm['airr'].fields))).
Unlike in #427 , I am on 0.13 and still suffer from the bug.

TypeError: Can't implicitly convert non-string objects to strings
Above error raised while writing key 'VJ_1_germline_alignment' of <class 'h5py._hl.group.Group'> to /

(it does this with many other columns, including all _call, _cigar columns)

To Reproduce

mdata = mu.MuData({'gex':adata.copy(),
       'tcr':tdata.copy(),
       'bcr':bdata.copy()})

ir.tl.chain_qc(mdata['tcr'])
ir.pp.ir_dist(mdata['tcr'], metric="hamming", sequence='nt', n_jobs=4, cutoff=20, key_added='ir_dist_nt_hamming_global')
ir.pp.ir_dist(mdata['tcr'], metric="identity", sequence='nt', n_jobs=4)

ir.tl.define_clonotypes(tdata, key_added='clone_id',
                        n_jobs=4, dual_ir='all', receptor_arms='all',
                        within_group=['receptor_type', 'donor_id_global'])

mdata['tcr'].obs = mdata['tcr'].obs.join(ir.get.airr(mdata['tcr'], mdata['tcr'].obsm['airr'].fields))

mdata.write(fname)

What else I've tried
Changing columns to categoricals

for mod in mdata.mod.keys():
    for col in mdata[mod].obs.columns:
        if re.findall(r'(V(?:D)?J_\d_\w_(?:call|cigar))', col):
            mdata[mod].obs[col] = mdata[mod].obs[col].astype('category')
            print(mod,':',col, sep='')
            
    mdata.update()

Expected behaviour
Save the file without problems

System

OS: Linux
Python version 3.9.16
Versions of libraries involved [Muon 0.1.5, Scirpy 0.13.0, Scanpy 1.9.3]

Additional context
Add any other context about the problem here.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the mdata.write(fname) call after joining ir.get.airr(...) into mdata['tcr'].obs, and inspect how the VJ_1_germline_alignment and _call or _cigar columns are written. Reproduce with the supplied MuData and Scirpy workflow; done means the resulting h5mu file saves without the TypeError.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
38/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.