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