XClone BAF xclone.pp.xclonedata > cell_anno.index.name = None

[stublakemore]

Dear Xianjie,

After spending a lot of time trying to resolve this issue myself, I wonder whether you can help me (again)!

Using Python3.9 and XClone v0.3.8 as per my other now resolved issues, when attempting to create the BAF_adata object using the xclone.pp.xclonedata function following the standard API documentation (https://xclone-cnv.readthedocs.io/en/latest/API.html#baf-module), I get the following error when running exactly this code:

BAF_adata = xclone.pp.xclonedata([AD_file, DP_file], 'BAF', mtx_barcodes_file, "hg19_genes", "Sample_6_BAF")

Traceback (most recent call last):
File "", line 1, in
File "/projects/mpi-sclc/sblakemo/anaconda3/envs/xclone/lib/python3.9/site-packages/xclone/preprocessing/_data.py", line 251, in xclonedata
cell_anno.index.name = None
UnboundLocalError: local variable 'cell_anno' referenced before assignment

Maybe there's something amiss with my .mtx objects, because I have 3 rather than two: cellSNP.tag.AD.mtx cellSNP.tag.DP.mtx cellSNP.tag.OTH.mtx, but running an adapted version of xclone.pp.xclonedata leads to the same error

BAF_adata = xclone.pp.xclonedata([AD_file, DP_file, OTH_file], 'BAF', mtx_barcodes_file, "hg19_genes", "Sample_6_BAF")
Traceback (most recent call last):
File "", line 1, in
File "/projects/mpi-sclc/sblakemo/anaconda3/envs/xclone/lib/python3.9/site-packages/xclone/preprocessing/_data.py", line 251, in xclonedata
cell_anno.index.name = None
UnboundLocalError: local variable 'cell_anno' referenced before assignment

I wondered whether I needed to initially load the features.tsv from the RDR analysis first as cell_anno, but that also kicks up the same error.

Following your intuition of looking at the log files, I inspected it, but don't seem to find anything that would mean my resolved xcltk issue actually isn't resolved? Please find the log file attached! You will surely identify something I can't!

Many thanks,

Stuart
pileup.log

[stublakemore]

Dear Xianjie,

I would really appreciate it if you could give me your insight on this! I don't have any further developments to report regarding either a solution or the cause of the issue.

Cheers,

Stuart

[hxj5]

Do you have any suggestions @Rongtingting?

[Rongtingting]

Hi Stuart,
@stublakemore
Could you try https://xclone-cnv.readthedocs.io/en/latest/preprocessing.html#baf-load this or attach the codes you used?
I am afraid that you did not specify the right path for the data files?

Bests,
Rongting

[stublakemore]

Dear Rongting,

Thanks for getting in touch. The exact codes I used is in my initial issue query at the top of the message chain. Specifically, I wonder whether it's a problem with the xlctk baf preprocessing, because not only do I have these file names rather than the readthedocs names: cellSNP.tag.AD.mtx cellSNP.tag.DP.mtx cellSNP.tag.OTH.mtx rather than "AD.mtx" & "DP.mtx", but I also rather have cellSNP.samples.tsv rather than "barcodes.tsv". I've tried taking the barcodes.tsv file from the RDR pre-processing object, without success... Below my code:

Attempt 1:

data_dir = "/projects/mpi-sclc/sblakemo/Sample_6/Sample_6_baf/pileup/"
AD_file = data_dir + "cellSNP.tag.AD.mtx"
DP_file = data_dir + "cellSNP.tag.DP.mtx"
mtx_barcodes_file = data_dir + "cellSNP.samples.tsv"
BAF_adata = xclone.pp.xclonedata([AD_file, DP_file], 'BAF',
... mtx_barcodes_file,
... genome_mode = "hg19_genes")
Traceback (most recent call last):
File "", line 1, in
File "/projects/mpi-sclc/sblakemo/anaconda3/envs/xclone/lib/python3.9/site-packages/xclone/preprocessing/_data.py", line 262, in xclonedata
Xadata = AnnData(AD, obs=cell_anno, var=regions_anno) # dtype='int32'
File "/projects/mpi-sclc/sblakemo/anaconda3/envs/xclone/lib/python3.9/site-packages/anndata/_core/anndata.py", line 254, in init
self._init_as_actual(
File "/projects/mpi-sclc/sblakemo/anaconda3/envs/xclone/lib/python3.9/site-packages/anndata/_core/anndata.py", line 428, in _init_as_actual
self._var = _gen_dataframe(
File "/projects/mpi-sclc/sblakemo/anaconda3/envs/xclone/lib/python3.9/functools.py", line 888, in wrapper
return dispatch(args[0].class)(*args, **kw)
File "/projects/mpi-sclc/sblakemo/anaconda3/envs/xclone/lib/python3.9/site-packages/anndata/_core/aligned_df.py", line 65, in _gen_dataframe_df
raise _mk_df_error(source, attr, length, len(anno))
ValueError: Observations annot. var must have as many rows as X has columns (1680), but has 32696 rows.

Attempt 2:

data_dir = "/projects/mpi-sclc/sblakemo/Sample_6/Sample_6_baf/pileup/"
AD_file = data_dir + "cellSNP.tag.AD.mtx"
DP_file = data_dir + "cellSNP.tag.DP.mtx"
mtx_barcodes_file = data_dir + "barcodes.tsv"
BAF_adata = xclone.pp.xclonedata([AD_file, DP_file], 'BAF',
... mtx_barcodes_file,
... genome_mode = "hg19_genes")
Traceback (most recent call last):
File "", line 1, in
File "/projects/mpi-sclc/sblakemo/anaconda3/envs/xclone/lib/python3.9/site-packages/xclone/preprocessing/_data.py", line 262, in xclonedata
Xadata = AnnData(AD, obs=cell_anno, var=regions_anno) # dtype='int32'
File "/projects/mpi-sclc/sblakemo/anaconda3/envs/xclone/lib/python3.9/site-packages/anndata/_core/anndata.py", line 254, in init
self._init_as_actual(
File "/projects/mpi-sclc/sblakemo/anaconda3/envs/xclone/lib/python3.9/site-packages/anndata/_core/anndata.py", line 428, in _init_as_actual
self._var = _gen_dataframe(
File "/projects/mpi-sclc/sblakemo/anaconda3/envs/xclone/lib/python3.9/functools.py", line 888, in wrapper
return dispatch(args[0].class)(*args, **kw)
File "/projects/mpi-sclc/sblakemo/anaconda3/envs/xclone/lib/python3.9/site-packages/anndata/_core/aligned_df.py", line 65, in _gen_dataframe_df
raise _mk_df_error(source, attr, length, len(anno))
ValueError: Observations annot. var must have as many rows as X has columns (1680), but has 32696 rows.

Here also the head of the AD matrix, which shows 4 columns but only containing 3 columns worth of data...
head cellSNP.tag.AD.mtx
%%MatrixMarket matrix coordinate integer general
%
1680 757 74066
1 6 1
1 42 1
1 43 1
1 51 1
1 90 1
1 118 1
1 120 1

which is the same for the DP matrix
%%MatrixMarket matrix coordinate integer general
%
1680 757 151948
1 6 1
1 12 2
1 25 1
1 42 1
1 43 1
1 49 1
1 51 1

If you need anything else from me to be able to resolve the issue, let me know and I'll look to provide further information!

Cheers,

Stuart