--- a
+++ b/useful_file/mouse_brain_preprocess.py
@@ -0,0 +1,135 @@
+import anndata as ad
+from scipy.sparse import csc_matrix, coo_matrix
+import numpy as np
+import pandas as pd
+
+###### preprcoess rna data
+
+adata = ad.read_text("./GSM4156610_brain.rna.counts.txt")
+adata = adata.transpose()
+X = csc_matrix(adata.X)
+obs = list(adata.obs.index)
+obs_new = []
+for n in obs:
+    n = n.replace(',','.')
+    obs_new.append(n)
+
+adata = ad.AnnData(X=X, obs=pd.DataFrame(index=obs_new), var=adata.var)
+adata.write("./rna_count.h5ad")
+
+del adata, X
+
+##### preprcoess atac data
+
+f = open('./GSM4156599_brain.barcodes.txt')
+obs_bc = []
+line = f.readline()
+obs_bc.append(line[:-1])
+while line:
+    line = f.readline()
+    if line=='':
+        break
+    obs_bc.append(line[:-1])
+
+f.close()
+
+f = open('./GSM4156599_brain.peaks.bed')
+var_name = []
+line = f.readline()
+var_name.append(('-').join(line.rstrip().split('\t')))
+while line:
+    line = f.readline()
+    if line=='':
+        break
+    var_name.append(('-').join(line.rstrip().split('\t')))
+
+f.close()
+
+f = open('./GSM4156599_brain.counts.txt')
+line = f.readline()
+line = f.readline()
+num_obs = int(line.split(' ')[1])
+num_var = int(line.split(' ')[0])
+row = []
+col = []
+value = []
+while line:
+    line = f.readline()
+    if line == '':
+        break
+    row.append(int(line.split(' ')[1]))
+    col.append(int(line.split(' ')[0]))
+    value.append(int(line.split(' ')[-1][:-1]))
+
+row = np.array(row)
+col = np.array(col)
+value = np.array(value)
+
+X = coo_matrix((value, (row-1,col-1)), shape=(num_obs, num_var))
+adata = ad.AnnData(X=X.tocsc(), obs=pd.DataFrame(index=obs_bc), var=pd.DataFrame(index=var_name))
+adata.write("./atac_count.h5ad")
+del adata, X
+
+#############################################################################################
+f = open('./GSM4156599_brain.barcodes.txt')
+obs_bc = []
+line = f.readline()
+obs_bc.append(line[:-1])
+while line:
+    line = f.readline()
+    if line=='':
+        break
+    obs_bc.append(line[:-1])
+
+f.close()
+
+
+f = open('./GSM4156599_brain_celltype.txt')
+line = f.readline()
+atac_bc = []
+rna_bc = []
+cell_type = []
+while line:
+    line = f.readline()
+    if line=='':
+        break
+    List = line.split('\t')
+    atac_bc.append(List[0])
+    rna_bc.append(List[1])
+    cell_type.append(List[2][:-1])
+
+f.close()
+rna2atac_bc = dict(zip(rna_bc, atac_bc))
+rna2celltype = dict(zip(rna_bc, cell_type))
+
+adata_gex = ad.read_h5ad("./rna_count.h5ad")
+adata_atac = ad.read_h5ad("./atac_count.h5ad")
+barcode_gex = list(adata_gex.obs.index)
+
+FLAG = []
+ATAC_barcode_new = []
+GEX_barcode_new = []
+Cell_type_new = []
+for sample in obs_bc:
+    FLAG.append(barcode_gex.index(sample))
+    ATAC_barcode_new.append(rna2atac_bc[sample])
+    GEX_barcode_new.append(sample)
+    Cell_type_new.append(rna2celltype[sample])
+
+X = adata_gex.X[np.array(FLAG)]
+var_name = list(adata_gex.var.index)
+adata = ad.AnnData(X=X, obs=pd.DataFrame(index=GEX_barcode_new), var=pd.DataFrame(index=var_name))
+adata.obs['cell_type'] = Cell_type_new
+adata.write("./rna_count_new.h5ad")
+
+X = adata_atac.X
+var_name = list(adata_atac.var.index)
+adata = ad.AnnData(X=X, obs=pd.DataFrame(index=ATAC_barcode_new), var=pd.DataFrame(index=var_name))
+adata.obs['cell_type'] = Cell_type_new
+adata.write("./atac_count_new.h5ad")
+
+############################################################################################
+adata_gex = ad.read_h5ad("./rna_count_new.h5ad")
+adata_atac = ad.read_h5ad("./atac_count_new.h5ad")
+
+