--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reformatPlatesLinearToTabular.pl	Wed Jun 01 03:55:27 2016 -0400
@@ -0,0 +1,99 @@
+###############################################################################
+# This script converts plate data from linear to tabular format.
+# 
+# Args:
+# input file: 
+# a text file containing a set of linear data in either 384/96 well format, 
+#
+# Returns:
+# For each input file, a tabular version of the data is returned
+# in the same format typically generated from synergy or cellomics software. 
+#
+# Author: jason ellul
+###############################################################################
+
+use strict;
+use warnings;
+use IO::Handle;
+use File::Temp qw/ tempfile tempdir /;
+my $tdir = tempdir( CLEANUP => 0 );
+
+# check to make sure having correct input and output files
+my $usage = "usage: reformatPlatesTabularToLinear.pl [TABULAR.in] [TABULAR.out] \n";
+die $usage unless @ARGV == 2;
+
+#get the input arguments
+my $linearPlateTable = $ARGV[0];
+my $tabularPlateTable =  $ARGV[1];
+
+#open the input files
+open (INPUT, "<", $linearPlateTable) || die("Could not open file $linearPlateTable \n");
+open (OUTPUT1, ">", $tabularPlateTable) || die("Could not open file $tabularPlateTable \n");
+
+#variable to store the name of the R script file
+my $r_script;
+
+# R script to implement the calcualtion of q-values based on multiple simultaneous tests p-values 	
+# construct an R script file and save it in a temp directory
+chdir $tdir;
+$r_script = "reformatPlatesLinearToTabular.r";
+
+open(Rcmd,">", $r_script) or die "Cannot open $r_script \n\n"; 
+print Rcmd "
+	#options(show.error.messages = FALSE);
+	
+	#read the plates table
+	#tables <- read.table(\"$linearPlateTable\", sep=\"\\t\", head=T, comment=\"\");
+	tablesTMP <- scan(\"$linearPlateTable\", sep=\"\\n\", what=\"character\", quiet = TRUE);
+	tmp <- strsplit(tablesTMP[1], \"\t\")[[1]];
+	tables <- matrix(\"\", nrow=length(tablesTMP)-1, ncol=length(tmp))
+	colnames(tables) <- tmp;
+	for(i in 2:length(tablesTMP)) {
+		tmp <- strsplit(tablesTMP[i], \"\t\")[[1]];
+		if(length(tmp) > ncol(tables)) stop(paste(\"Error: Row\", i, \"has more columns than the header\"));
+		tables[i-1, 1:length(tmp)] <- tmp;
+	}
+	tables <- as.data.frame(tables, stringsAsFactors=F);
+	
+	if(ncol(tables) < 2) {
+		stop(\"The first column of the table must contain the well ID from A01 to either H12 or P24 depending on the number of wells.\")
+	}
+
+	# check if the plate is in 96 or 384 well format
+	if(nrow(tables) == 96) {
+		nc <- 12;
+		nr <- 8;	
+	} else if(nrow(tables) == 384) {
+		nc <- 24;
+		nr <- 16;
+	} else {
+		stop(\"Table is not for a 96 or 384 well plate. Please ensure you either have 96 or 384 rows plus a header.\")
+	}
+
+	# for each table
+	for(i in 2:ncol(tables)) {
+		# write the name of the table
+		write(paste(colnames(tables)[i], sep=\"\"), file=\"$tabularPlateTable\", append=T);
+		write(\"\", file=\"$tabularPlateTable\", append=T);
+		# the column header
+		write(paste(\"\\t\", paste(1:nc, collapse=\"\\t\"), sep=\"\"), file=\"$tabularPlateTable\", append=T);
+		# replace any NAs with blank
+		if(any(is.na(tables[,i]))) tables[which(is.na(tables[,i])),i] <- \"\";
+		# for each row print the values
+		curr <- 0;
+		for(j in LETTERS[1:nr]) {
+			write(paste(j, \"\\t\", paste(tables[(curr+1):(curr+nc), i], collapse=\"\\t\"), sep=\"\"), file=\"$tabularPlateTable\", append=T);
+			curr <- curr + nc;
+		}
+		# if we are at the last table do not add an extra line
+		if(i != ncol(tables)) write(\"\", file=\"$tabularPlateTable\", append=T);
+	}
+	#eof\n";
+
+close Rcmd;	
+
+system("R --no-restore --no-save --no-readline < $r_script > $r_script.out");
+
+#close the input and output files
+close(OUTPUT1);
+close(INPUT);