diff t_test_two_samples.pl @ 0:3d24b35de20a draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/t_test_two_samples.pl	Wed Aug 21 10:58:59 2013 -0400
@@ -0,0 +1,109 @@
+# A program to implement the non-pooled t-test for two samples where the alternative hypothesis is two-sided or one-sided. 
+# The first input file is a TABULAR format file representing the first sample and consisting of one column only.
+# The second input file is a TABULAR format file representing the first sample nd consisting of one column only.
+# The third input is the sidedness of the t-test: either two-sided or, one-sided with m1 less than m2 or, 
+# one-sided with m1 greater than m2. 
+# The fourth input is the equality status of the standard deviations of both populations
+# The output file is a TXT file representing the result of the two sample t-test.
+
+use strict;
+use warnings;
+
+#variable to handle the motif information
+my $motif;
+my $motifName = "";
+my $motifNumber = 0;
+my $totalMotifsNumber = 0;
+my @motifNamesArray = ();
+
+# check to make sure having correct files
+my $usage = "usage: non_pooled_t_test_two_samples_galaxy.pl [TABULAR.in] [TABULAR.in] [testSidedness] [standardDeviationEquality] [TXT.out] \n";
+die $usage unless @ARGV == 5;
+
+#get the input arguments
+my $firstSampleInputFile = $ARGV[0];
+my $secondSampleInputFile = $ARGV[1];
+my $testSidedness = $ARGV[2];
+my $standardDeviationEquality = $ARGV[3]; 
+my $outputFile = $ARGV[4];
+
+#open the input files
+open (INPUT1, "<", $firstSampleInputFile) || die("Could not open file $firstSampleInputFile \n"); 
+open (INPUT2, "<", $secondSampleInputFile) || die("Could not open file $secondSampleInputFile \n"); 
+open (OUTPUT, ">", $outputFile) || die("Could not open file $outputFile \n");
+
+
+#variables to store the name of the R script file
+my $r_script;
+	
+# R script to implement the two-sample test on the motif frequencies in upstream flanking region 	
+#construct an R script file and save it in the same directory where the perl file is located
+$r_script = "non_pooled_t_test_two_samples.r";
+
+open(Rcmd,">", $r_script) or die "Cannot open $r_script \n\n";
+print Rcmd "
+        sampleTable1 <- read.table(\"$firstSampleInputFile\", header=FALSE);
+		sample1 <- sampleTable1[, 1];
+		
+		sampleTable2 <- read.table(\"$secondSampleInputFile\", header=FALSE);
+		sample2 <- sampleTable2[, 1];
+		
+		testSideStatus <- \"$testSidedness\";
+		STEqualityStatus <- \"$standardDeviationEquality\";
+		
+		#open the output a text file
+		sink(file = \"$outputFile\");
+		
+		#check if the t-test is two-sided
+		if (testSideStatus == \"two-sided\"){
+			
+			#check if the standard deviations are equal in both populations
+			if (STEqualityStatus == \"equal\"){
+				#two-sample t-test where standard deviations are assumed to be unequal, the test is two-sided
+				testResult <- t.test(sample1, sample2, var.equal = TRUE);	
+			} else{
+				#two-sample t-test where standard deviations are assumed to be unequal, the test is two-sided
+				testResult <- t.test(sample1, sample2, var.equal = FALSE);
+			}
+		} else{  #the t-test is one sided	
+			
+			#check if the t-test is two-sided with m1 < m2
+			if (testSideStatus == \"one-sided:_m1_less_than_m2\"){
+				
+				#check if the standard deviations are equal in both populations
+				if (STEqualityStatus == \"equal\"){
+					#two-sample t-test where standard deviations are assumed to be unequal, the test is one-sided: Halt: m1 < m2
+					testResult <- t.test(sample1, sample2, var.equal = TRUE, alternative = \"less\");
+				} else{
+					#two-sample t-test where standard deviations are assumed to be unequal, the test is one-sided: Halt: m1 < m2
+					testResult <- t.test(sample1, sample2, var.equal = FALSE, alternative = \"less\");
+				}
+			} else{   #the t-test is one-sided with m1 > m2
+				#check if the standard deviations are equal in both populations
+				if (STEqualityStatus == \"equal\"){
+					#two-sample t-test where standard deviations are assumed to be unequal, the test is one-sided: Halt: m1 < m2
+					testResult <- t.test(sample1, sample2, var.equal = TRUE, alternative = \"greater\");
+				} else{
+					#two-sample t-test where standard deviations are assumed to be unequal, the test is one-sided: Halt: m1 < m2
+					testResult <- t.test(sample1, sample2, var.equal = FALSE, alternative = \"greater\");
+				}
+			}
+		}
+		
+		#save the output of the t-test into the output text file
+		testResult;
+		
+		#close the output text file
+		sink();
+		
+		#eof" . "\n";
+		
+close Rcmd;	
+
+system("R --no-restore --no-save --no-readline < $r_script > $r_script.out");
+
+#close the input and output files
+close(OUTPUT);
+close(INPUT2);
+close(INPUT1);
+