diff --git a/read_data.R b/read_data.R
index 23ae796..97c8c78 100644
--- a/read_data.R
+++ b/read_data.R
@@ -8,14 +8,23 @@ getwd()
 # load libraries, packages and local imports
 source("Header_TT.R")
 ########################################################################
-# TODO: turn this to a repo
+maindir = "~/git/mosaic_2020/"
+outdir = paste0(maindir, "output/")
+ifelse(!dir.exists(outdir), dir.create(outdir), FALSE)
+
+outdir_stats = "~/git/mosaic_2020/output/stats/"
+ifelse(!dir.exists(outdir_stats), dir.create(outdir_stats), FALSE)
+
+outdir_plots = "~/git/mosaic_2020/output/plots/"
+ifelse(!dir.exists(outdir_plots), dir.create(outdir_plots), FALSE)
+########################################################################
+# static file read: csv
+#==============
+# all patients
+#==============
 all_df <- read.csv("/home/backup/MOSAIC/MEDIATOR_Data/master_file/Mosaic_master_file_from_stata.csv"
                    , fileEncoding='latin1') 
 
-hc_data<- read.csv("/home/backup/MOSAIC/MEDIATOR_Data/master_file/Mediators_for_HC.csv")
-str(hc_data)
-table(hc_data$Timepoint, hc_data$Sample)
-
 # meta data columns                   
 meta_data_cols = c("mosaic", "gender", "age", "adult", "flustat", "type"
                    , "obesity", "obese2", "height", "height_unit", "weight"
@@ -26,13 +35,11 @@ meta_data_cols%in%colnames(all_df)
 all(meta_data_cols%in%colnames(all_df))
 
 metadata_all = all_df[, meta_data_cols]
-########################################################################
-outdir = "~/git/mosaic_2020/output/"
-ifelse(!dir.exists(outdir), dir.create(outdir), FALSE)
 
-outdir_stats = "~/git/mosaic_2020/output/stats/"
-ifelse(!dir.exists(outdir_stats), dir.create(outdir_stats), FALSE)
-
-outdir_plots = "~/git/mosaic_2020/output/plots/"
-ifelse(!dir.exists(outdir_plots), dir.create(outdir_plots), FALSE)
+#============
+# hc
+#============
+#hc_data<- read.csv("/home/backup/MOSAIC/MEDIATOR_Data/master_file/Mediators_for_HC.csv")
+#str(hc_data)
+#table(hc_data$Timepoint, hc_data$Sample)
 ########################################################################