Bugs in 'pp.check_contigs'
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chf8991 commented
Description of the bug
When running 'pp.check_contigs' with default sets, I got the following error 'local variable "vdj_ccall_p_igm_count" referenced before assignment'. But the 'pp.filter_contigs' function works fine.
Minimal reproducible example
bcr_vdj, adata_BP = ddl.pp.check_contigs(bcr_vdj, adata_BP)The error message produced by the code above
Preparing data: 267882it [01:44, 2568.34it/s]
Scanning for poor quality/ambiguous contigs: 0%| | 1/220792 [00:00<23:15, 158.23it/s]
---------------------------------------------------------------------------
UnboundLocalError Traceback (most recent call last)
Cell In[53], line 1
----> 1 bcr_vdj, adata_BP = ddl.pp.check_contigs(bcr_vdj, adata_BP)
2 #>local variable 'vdj_ccall_p_igm_count' referenced before assignment
File ~/.conda/envs/dandelion/lib/python3.9/site-packages/dandelion/preprocessing/_preprocessing.py:5199, in check_contigs(data, adata, productive_only, library_type, umi_foldchange_cutoff, filter_missing, filter_extra, save, verbose, **kwargs)
5197 adata_ = ad.AnnData(obs=obs)
5198 adata_.obs["has_contig"] = "True"
-> 5199 contig_status = MarkAmbiguousContigs(dat, umi_foldchange_cutoff, verbose)
5201 ambigous = contig_status.ambiguous_contigs.copy()
5202 extra = contig_status.extra_contigs.copy()
File ~/.conda/envs/dandelion/lib/python3.9/site-packages/dandelion/preprocessing/_preprocessing.py:5387, in MarkAmbiguousContigs.__init__(self, data, umi_foldchange_cutoff, verbose)
5376 vdj_ccall_p_igm_count = dict(
5377 data1[data1["c_call"] == "IGHM"][
5378 "umi_count"
5379 ]
5380 )
5381 vdj_ccall_p_igd_count = dict(
5382 data1[data1["c_call"] == "IGHD"][
5383 "umi_count"
5384 ]
5385 )
-> 5387 if len(vdj_ccall_p_igm_count) > 1:
5388 (
5389 keep_igm,
5390 extra_igm,
(...)
5394 umi_foldchange_cutoff,
5395 )
5396 else:
UnboundLocalError: local variable 'vdj_ccall_p_igm_count' referenced before assignmentOS information
No response
Version information
dandelion==0.3.5 pandas==2.2.0 numpy==1.26.4 matplotlib==3.8.4 networkx==3.1 scipy==1.13.0
Additional context
No response