improve wrapper.R to handle files too

diff --git a/code/stage1/wrapper.R b/code/stage1/wrapper.R
index e1fa30e..524fc90 100644 (file)
--- a/code/stage1/wrapper.R
+++ b/code/stage1/wrapper.R
@@ -5,9 +5,16 @@ ppam_exe = function(path=".", np=parallel::detectCores(), data=NULL, args="DontL
        #if data provided (as data.frame or matrix...): binarize it, and add it as first argument
        if (!is.null(data))
        {
-               write.csv(data, "/tmp/data_csv")
-               system(paste(path,"/ppam.exe serialize /tmp/data_csv /tmp/data_bin 0 0",sep=""))
-               command_line = paste(command_line," ","/tmp/data_bin",sep="")
+               if (!is.character(data))
+               {
+                       #assuming matrix or data.frame, WITH row names (identifiers; could be line number...)
+                       write.csv(data, "/tmp/data_csv", row.names=TRUE, col.names=FALSE)
+                       system(paste(path,"/ppam.exe serialize /tmp/data_csv /tmp/data_bin 0 0",sep=""))
+               } else
+               {
+                       system(paste(path,"/ppam.exe serialize ",data," /tmp/data_bin 0 0",sep=""))
+               }
+               command_line = paste(command_line," /tmp/data_bin",sep="")
        }
 
        command_line = paste(command_line," ",args,sep="")