Use TPM_FILE instead of TPM_TABLE

2 files changed, 3 insertions, 21 deletions

diff --git a/Code/buildRmatrix.py b/Code/buildRmatrix.py
index 363e0a3..1c90eb0 100644
--- a/Code/buildRmatrix.py
+++ b/Code/buildRmatrix.py
@@ -10,8 +10,9 @@
 # Last modified 10 Oct 2020, hui, zjnu [note that if there are more than 1000 RNA-seq samples, this script requires at least 7GB memory to run.]

 

 import os, sys, glob

+from configure import TPM_FILE

 

-TPM_TABLE = '../Data/history/expr/TPM.txt'

+TPM_TABLE = TPM_FILE

 WARN_NA   = False

 

 ####################################

@@ -239,4 +240,4 @@ global_param_dict = make_global_param_dict(param_file)
 data_dict = make_data_dict(param_file)

 TPM_TABLE = os.path.abspath(TPM_TABLE)

 save_TPM_table(get_gene_list(global_param_dict['GENE_LIST']), get_dict_list(data_dict), TPM_TABLE)

-#print('Done.  Check %s.' % (TPM_TABLE))

+

diff --git a/Code/slice_TPM_to_JSON.R b/Code/slice_TPM_to_JSON.R
deleted file mode 100644
index fb7a39d..0000000
--- a/Code/slice_TPM_to_JSON.R
+++ /dev/null
@@ -1,19 +0,0 @@
-
-library(rjson)
-dir.name <- '../Data/history/expr/json'
-tpm.file <- '../Data/history/expr/TPM.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,])
-    file.name = paste(dir.name, paste(gene.id[i], 'json', sep='.'), sep='/')
-    cat(y, file=file.name)
-}