huangyh09
commented
1 year ago Hi,
Thanks for sharing the issue and sorry for the delay in getting back. After some diagnosis, it looks like an uncommon issue when the donor file uses “chr” and the cell file doesn’t, and the SNPs are only partially matched.
Here, I made a quick fix in the new release v0.5.8. Please upgrade and try it again, and see if it resolves the issue.
pip install -U vireoSNPYuanhua
I generated a cellSNP vcf file from snRNA-Seq comprised of three different donors. I'd like to identify the barcodes belonging to one of the donors using its corresponding genotype. I recently tried to run vireo using the cellSNP vcf and the genotype vcf from one of the donors to identify which barcodes belonged to that donor. However, I received an error from the match_donor_VCF() function, defined in io_utils.py, that the match() function output mm_idx is a NoneType and can't be contrasted to an int class by >=.
The script I ran:
CELL_DATA=/u/home/a/alexiswe/project-dhg/CellSNPRun/Ctrl0512CellSNPOut/total_chroms_cellsY.vcf.gz DONOR_GT_FILE=/u/home/a/alexiswe/project-dhg/111822GenotypePlinkables/PLINK_050123_0406_B07_N1644/N1644.vcf.gz OUT_DIR=/u/home/a/alexiswe/project-dhg/CtrlMultiomeVireoOut/Ctrl0512VireoOut/u/home/a/alexiswe/.local/bin/vireo -c $CELL_DATA -d $DONOR_GT_FILE -o $OUT_DIR -N $n_donor -t GTThe error I received:
[vireo] Loading cell VCF file ... [vireo] Loading donor VCF file ... Traceback (most recent call last): File "/u/home/a/alexiswe/.local/bin/vireo", line 33, in <module> sys.exit(load_entry_point('vireoSNP==0.5.6', 'console_scripts', 'vireo')()) File "/u/home/a/alexiswe/.local/lib/python3.9/site-packages/vireoSNP/vireo.py", line 160, in main cell_dat, donor_vcf = match_donor_VCF(cell_dat, donor_vcf) File "/u/home/a/alexiswe/.local/lib/python3.9/site-packages/vireoSNP/utils/io_utils.py", line 20, in match_donor_VCF if np.sum(mm_idx == mm_idx) == 0 or np.sum(mm_idx >= 0) == 0: TypeError: '>=' not supported between instances of 'NoneType' and 'int'