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Fix bug of negative count value generated by scatac-peakcount #123

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Fix bug of negative count value generated by scatac-peakcount #123

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4 changes: 2 additions & 2 deletions MAESTRO/scATAC_10x_PeakCount.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
# @E-mail: [email protected]
# @Date: 2020-02-24 22:26:54
# @Last Modified by: Dongqing Sun
# @Last Modified time: 2020-12-13 20:46:06
# @Last Modified time: 2021-03-15 22:30:19

import os,sys
import time
Expand Down Expand Up @@ -119,7 +119,7 @@ def generate_count_matrix(count_list, peak_list, binary = False):

peak_count = {}
for peak in peak_list:
peak_count[peak] = sp_sparse.dok_matrix((1, len(count_list)), dtype=np.int8)
peak_count[peak] = sp_sparse.dok_matrix((1, len(count_list)), dtype=np.int32)

barcodes = []
for i in range(0,len(count_list)):
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4 changes: 2 additions & 2 deletions MAESTRO/scATAC_H5Process.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
# @E-mail: [email protected]
# @Date: 2020-02-23 19:44:05
# @Last Modified by: Dongqing Sun
# @Last Modified time: 2020-11-02 22:31:18
# @Last Modified time: 2021-03-15 22:31:14


import os
Expand Down Expand Up @@ -196,7 +196,7 @@ def write_10X_h5(filename, matrix, features, barcodes, genome = 'GRCh38', dataty
"""Write 10X HDF5 files, support both gene expression and peaks."""
f = h5py.File(filename, 'w')
if datatype == 'Peak':
M = sp_sparse.csc_matrix(matrix, dtype=numpy.int8)
M = sp_sparse.csc_matrix(matrix, dtype=numpy.int32)
else:
M = sp_sparse.csc_matrix(matrix, dtype=numpy.float32)
B = numpy.array(barcodes, dtype='|S200')
Expand Down