Check if cell data has any variant and check if cell data variants ha… #108
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…ve any overlap with donor VCF file.
Check if cell data has any variant and check if cell data variants
have any overlap with donor VCF file.
Examples:
- Running vireo with a cellSNP directory that does not have any variant
(as provided CBs for cellSNP-lite did not overlap with any variants).
[vireo] Loading cell folder ...
Error: cell data in vcf file, or cellSNP output folder, or vartrix's alt.mtx,ref.mtx,barcodes.tsv does not contain any variants.
- Running vireo with a VCF file that does not overlap at all with the
SNPs used in cellSNP-lite.
[vireo] Loading cell folder ...
[vireo] Loading donor VCF file ...
/conda/envs/cellsnp/lib/python3.11/site-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice.
return _methods._mean(a, axis=axis, dtype=dtype,
/conda/envs/cellsnp/lib/python3.11/site-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide
ret = ret.dtype.type(ret / rcount)
[vireo] warning: no variants matched to donor VCF, please check chr format!
Error: No matching variants found between cell data and donor VCF.
Before:
[vireo] Loading cell folder ...
[vireo] Loading donor VCF file ...
/conda/envs/cellsnp/lib/python3.11/site-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice.
return _methods._mean(a, axis=axis, dtype=dtype,
/conda/envs/cellsnp/lib/python3.11/site-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide
ret = ret.dtype.type(ret / rcount)
[vireo] warning: no variants matched to donor VCF, please check chr format!
Traceback (most recent call last):
File "/conda/envs/cellsnp/bin/vireo", line 8, in <module>
sys.exit(main())
^^^^^^
File "/conda/envs/cellsnp/lib/python3.11/site-packages/vireoSNP/vireo.py", line 168, in main
donor_GPb = parse_donor_GPb(donor_vcf['GenoINFO'][options.geno_tag],
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/conda/envs/cellsnp/lib/python3.11/site-packages/vireoSNP/utils/vcf_utils.py", line 328, in parse_donor_GPb
GT_prob = np.zeros((len(GT_dat), len(GT_dat[0]), 3))
~~~~~~^^^
IndexError: list index out of range
The traceback obscures the warning message.
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…ve any overlap with donor VCF file.
Check if cell data has any variant and check if cell data variants have any overlap with donor VCF file.
Examples:
Running vireo with a cellSNP directory that does not have any variant (as provided CBs for cellSNP-lite did not overlap with any variants).
[vireo] Loading cell folder ... Error: cell data in vcf file, or cellSNP output folder, or vartrix's alt.mtx,ref.mtx,barcodes.tsv does not contain any variants.
Running vireo with a VCF file that does not overlap at all with the SNPs used in cellSNP-lite.
cellSNP-lite [vireo] Loading cell folder ... [vireo] Loading donor VCF file ... /conda/envs/cellsnp/lib/python3.11/site-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice. return _methods._mean(a, axis=axis, dtype=dtype, /conda/envs/cellsnp/lib/python3.11/site-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide ret = ret.dtype.type(ret / rcount) [vireo] warning: no variants matched to donor VCF, please check chr format! Error: No matching variants found between cell data and donor VCF.
Before: