Genotype-free demultiplexing of pooled single-cell RNA-Seq, using a hidden state model for identifying genetically distinct samples within a mixed population.
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AttributeError: 'DataFrame' object has no attribute 'ix' #14
looks like current scSplit using an older version of indexing using .ix instead of .loc. I got error message
warnings.warn(
Traceback (most recent call last):
File "/sfs/qumulo/qhome/yh9fj/.local/lib/python3.8/site-packages/scSplit/scSplit", line 642, in
scSplit()
File "/sfs/qumulo/qhome/yh9fj/.local/lib/python3.8/site-packages/scSplit/scSplit", line 354, in init
getattr(self, args.command)()
File "/sfs/qumulo/qhome/yh9fj/.local/lib/python3.8/site-packages/scSplit/scSplit", line 525, in run
model.distinguishing_alleles(pos)
File "/sfs/qumulo/qhome/yh9fj/.local/lib/python3.8/site-packages/scSplit/scSplit", line 280, in distinguishing_alleles
alt_or_ref = alt_or_ref.ix[[x for x in alt_or_ref.index if x[0] not in ['X','Y','MT']]]
File "/apps/software/standard/core/anaconda/2020.11-py3.8/lib/python3.8/site-packages/pandas/core/generic.py", line 5139, in getattr
return object.getattribute(self, name)
AttributeError: 'DataFrame' object has no attribute 'ix'
This is my code --
python $dir_scSplit/scSplit run --r $dir_vcf/ref_filtered.csv -a $dir_vcf/alt_filtered.csv -n 2
I have updated pandas to 1.3.3
Thanks
-Yong
yh9fj@virginia.edu
looks like current scSplit using an older version of indexing using .ix instead of .loc. I got error message warnings.warn( Traceback (most recent call last): File "/sfs/qumulo/qhome/yh9fj/.local/lib/python3.8/site-packages/scSplit/scSplit", line 642, in
scSplit()
File "/sfs/qumulo/qhome/yh9fj/.local/lib/python3.8/site-packages/scSplit/scSplit", line 354, in init
getattr(self, args.command)()
File "/sfs/qumulo/qhome/yh9fj/.local/lib/python3.8/site-packages/scSplit/scSplit", line 525, in run
model.distinguishing_alleles(pos)
File "/sfs/qumulo/qhome/yh9fj/.local/lib/python3.8/site-packages/scSplit/scSplit", line 280, in distinguishing_alleles
alt_or_ref = alt_or_ref.ix[[x for x in alt_or_ref.index if x[0] not in ['X','Y','MT']]]
File "/apps/software/standard/core/anaconda/2020.11-py3.8/lib/python3.8/site-packages/pandas/core/generic.py", line 5139, in getattr
return object.getattribute(self, name)
AttributeError: 'DataFrame' object has no attribute 'ix'
This is my code -- python $dir_scSplit/scSplit run --r $dir_vcf/ref_filtered.csv -a $dir_vcf/alt_filtered.csv -n 2
I have updated pandas to 1.3.3 Thanks -Yong yh9fj@virginia.edu