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| f_prepare4CSOmap <- function(lc_scRNA, lc_csomap_data_dir, lc_className){
lc_csomap_data_dir <- system(paste("echo", lc_csomap_data_dir), intern = T)
if(!file.exists(lc_csomap_data_dir)){dir.create(lc_csomap_data_dir)}
# 导出label.txt
labels <- lc_scRNA[[lc_className]]
labels$cells <- gsub("-", "." ,rownames(labels)) # TPM的colnames 不知为何导出时被替换了，这里也替换一下
labels$labels <- as.character(labels[[lc_className]])
rownames(labels) <- NULL
labels = labels[,c("cells", "labels")]
write.table(labels, file.path(lc_csomap_data_dir, "label.txt"), row.names = F, sep = "\t", quote = F) # 不要引号
# copy LR_pairs.txt
file.copy(from = file.path(lc_csomap_data_dir,"..","demo","LR_pairs.txt"), to = file.path(lc_csomap_data_dir, "LR_pairs.txt"))
# 导出TPM.txt
tpm <- exp(lc_scRNA[['RNA']]@data)
tpm <- tpm - 1
tpm <- tpm*100 # 1E4 to 1E6
colnames(tpm)[1] = paste0('T', colnames(tpm)[1]) # 预留\t位置
write.table(tpm, file.path(lc_csomap_data_dir, "TPM.txt"), sep = "\t", quote = F) # 不要引号
lc_fix <- tempfile()
lc_py <- sprintf('
import mmap, os
def mapfile(filename, *args, size=None, **kwargs):
file = open(filename, *args, **kwargs)
if size is None: size = os.path.getsize(filename)
return mmap.mmap(file.fileno(), size)
path = "%s"
print(path, "%s")
f = mapfile(path,"r+", size=10)
f[0:1] = b"\t"
print(f[:])
f.close()
print("Done")
', file.path(lc_csomap_data_dir, "TPM.txt"), lc_fix)
print(lc_py)
cat(file=lc_fix, lc_py)
print(system(paste("python3", lc_fix), intern = T))
}
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