Use R package jsonlite instead of rjson, to support the 'digits' option, which allows keeping fewer digits after decimal, thus saving disk storage space

3 files changed, 41 insertions, 2 deletions

diff --git a/Code/getTF.py b/Code/getTF.py
new file mode 100644
index 0000000..1090bd2
--- /dev/null
+++ b/Code/getTF.py
@@ -0,0 +1,19 @@
+import json
+
+tfs = set()
+
+with open('../Data/information/target_tf.txt') as f:
+    for line in f:
+        line = line.strip()
+        lst = line.split('\t')
+        tf = lst[1]
+        tfs.add(tf)
+
+with open('../Data/information/target_tf_agris.txt') as f:
+    for line in f:
+        line = line.strip()
+        lst = line.split('\t')
+        tf = lst[1]
+        tfs.add(tf)
+
+print(json.dumps(sorted(list(tfs))))
diff --git a/Code/slice_TPM_to_JSON.R b/Code/slice_TPM_to_JSON.R
new file mode 100644
index 0000000..e7021ef
--- /dev/null
+++ b/Code/slice_TPM_to_JSON.R
@@ -0,0 +1,20 @@
+
+#library(rjson)
+library(jsonlite)
+dir.name <- '../Data/history/expr/json'
+tpm.file <- '../Data/history/expr/assemble/TPM.6604.txt'
+take.log <- 'YES'
+X <- read.table(tpm.file, header=T, check.names=FALSE, sep="\t")
+gene.id <- as.vector(X[,1])
+X[,1] <- NULL # remove first column
+if (take.log == 'YES') {
+    X <- log(X+1)
+}
+if (!dir.exists(dir.name)) {
+    dir.create(dir.name)
+}
+for (i in 1:dim(X)[1]) {
+            y <- toJSON(X[i,], digits=I(3))
+    file.name = paste(dir.name, paste(gene.id[i], 'json', sep='.'), sep='/')
+    cat(y, file=file.name)
+}
diff --git a/Code/slice_TPM_to_JSON.py b/Code/slice_TPM_to_JSON.py
index e597b78..618310f 100644
--- a/Code/slice_TPM_to_JSON.py
+++ b/Code/slice_TPM_to_JSON.py
@@ -127,7 +127,7 @@ def make_json_file(expr_dict, dir_name, glb_param_dict):
 
 def make_json_file_using_r(dir_name, glb_param_dict): # use r script to make it faster
     r_code = '''
-	library(rjson)
+	library(jsonlite)
 	dir.name <- '%s'
 	tpm.file <- '%s'
 	take.log <- '%s'
@@ -141,7 +141,7 @@ def make_json_file_using_r(dir_name, glb_param_dict): # use r script to make it
 	    dir.create(dir.name)
 	}
 	for (i in 1:dim(X)[1]) {
-	    y <- toJSON(X[i,])
+	    y <- toJSON(X[i,], digits=I(3))
 	    file.name = paste(dir.name, paste(gene.id[i], 'json', sep='.'), sep='/')
 	    cat(y, file=file.name)
 	}