include miRNA and handel -10 in RNASeq

tool-data/Rscripts/Create_MarkerSelection_inputfile.pl

@@ -5,8 +5,8 @@
 ## Description: Merges the two subset mrna.tsv subset files ##
 ## and puts the data into the correct format to be used     ##
 ## as input by MarkerSelection.R                            ##
-## Usage: Create_GEX_outputfile.pl -s1 <subset1_input_file> ##
-##        -s2 <subset2_input_file> -dir <in/output dir>     ##
+## Usage: Create_GEX_outputfile.pl <subset1_input_file>     ##
+##        <subset2_input_file> <in/output dir> <data_filter>##
 ## Email: serge.eifes@uni.lu                                ##
 ##                                                          ##
 ## This work is licensed under the Creative Commons         ##
@@ -26,7 +26,10 @@ use warnings;
 my $file_1=$ARGV[0];
 my $file_2=$ARGV[1];
 my $O_file=$ARGV[2];
+#my $data_filter=$ARGV[3]; #Should be either "TRUE" or "FALSE". All values corresponding to -10 will be set to NA
+my $data_filter="TRUE"; # test Wei
 
+die "Not allowed argument: $data_filter. Value provided should be 'TRUE' or 'FALSE'" if(($data_filter ne "TRUE") && ($data_filter ne "FALSE"));
 
 
 my @A_Subset_files;
@@ -73,7 +76,10 @@ foreach my $file (@A_Subset_files){
 					$Probe_ID_idx = $i;
 				} elsif($A_Line[$i] eq "GENE SYMBOL"){
 					$Gene_Symbol_idx = $i;
-				}
+				} elsif($A_Line[$i] eq "MIRNA ID"){
+					$Probe_ID_idx = $i;
+					$Gene_Symbol_idx = $i;
+				} 
 			}
 			next;
 		}
@@ -83,6 +89,10 @@ foreach my $file (@A_Subset_files){
 		my $Probe_ID = $A_Line[$Probe_ID_idx];
 		my $Gene_Symbol = $A_Line[$Gene_Symbol_idx];
 		
+		if($data_filter eq "TRUE"){
+			$Value="NA" if$Value==-10;
+		}
+		
 		$Gene_Symbol="NA" if($Gene_Symbol eq "null");
 		
 		my $Subset;