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Error in st.cal_qc
my code is :
import stream as st
adata=st.read(file_name='/outs/filtered_peak_bc_matrix/matrix.mtx',
file_sample='/outs/filtered_peak_bc_matrix/barcodes.tsv',
file_feature='/outs/filtered_peak_bc_matrix/peaks.bed',
file_format='mtx',workdir='./result_atac')
adata.var.index =adata.var[0].astype(str) + '' + adata.var[1].astype(str) +'' + adata.var[2].astype(str)
st.cal_qc(adata2,assay='atac')
the error is :
ValueError Traceback (most recent call last)
/tmp/ipykernel_352024/3261032759.py in
~/app/ENTER/envs/stream1/lib/python3.7/site-packages/stream/core.py in cal_qc(adata, expr_cutoff, assay) 438 439 n_counts = adata.X.sum(axis=0) --> 440 adata.var['n_counts'] = n_counts 441 n_cells = (adata.X>=expr_cutoff).sum(axis=0) 442 adata.var['n_cells'] = n_cells
~/app/ENTER/envs/stream1/lib/python3.7/site-packages/pandas/core/frame.py in setitem(self, key, value) 3610 else: 3611 # set column -> 3612 self._set_item(key, value) 3613 3614 def _setitem_slice(self, key: slice, value):
~/app/ENTER/envs/stream1/lib/python3.7/site-packages/pandas/core/frame.py in _set_item(self, key, value) 3782 ensure homogeneity. 3783 """ -> 3784 value = self._sanitize_column(value) 3785 3786 if (
~/app/ENTER/envs/stream1/lib/python3.7/site-packages/pandas/core/frame.py in _sanitize_column(self, value) 4507 4508 if is_list_like(value): -> 4509 com.require_length_match(value, self.index) 4510 return sanitize_array(value, self.index, copy=True, allow_2d=True) 4511
~/app/ENTER/envs/stream1/lib/python3.7/site-packages/pandas/core/common.py in require_length_match(data, index) 530 if len(data) != len(index): 531 raise ValueError( --> 532 "Length of values " 533 f"({len(data)}) " 534 "does not match length of index "
ValueError: Length of values (1) does not match length of index (156605)
my package version is: