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1 # 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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2 # The first input file is a TABULAR format file representing the first sample and consisting of one column only.
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3 # The second input file is a TABULAR format file representing the first sample nd consisting of one column only.
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4 # 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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5 # one-sided with m1 greater than m2.
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6 # The fourth input is the equality status of the standard deviations of both populations
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7 # The output file is a TXT file representing the result of the two sample t-test.
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8
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9 use strict;
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10 use warnings;
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11
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12 #variable to handle the motif information
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13 my $motif;
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14 my $motifName = "";
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15 my $motifNumber = 0;
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16 my $totalMotifsNumber = 0;
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17 my @motifNamesArray = ();
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18
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19 # check to make sure having correct files
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20 my $usage = "usage: non_pooled_t_test_two_samples_galaxy.pl [TABULAR.in] [TABULAR.in] [testSidedness] [standardDeviationEquality] [TXT.out] \n";
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21 die $usage unless @ARGV == 5;
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22
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23 #get the input arguments
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24 my $firstSampleInputFile = $ARGV[0];
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25 my $secondSampleInputFile = $ARGV[1];
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26 my $testSidedness = $ARGV[2];
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27 my $standardDeviationEquality = $ARGV[3];
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28 my $outputFile = $ARGV[4];
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29
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30 #open the input files
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31 open (INPUT1, "<", $firstSampleInputFile) || die("Could not open file $firstSampleInputFile \n");
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32 open (INPUT2, "<", $secondSampleInputFile) || die("Could not open file $secondSampleInputFile \n");
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33 open (OUTPUT, ">", $outputFile) || die("Could not open file $outputFile \n");
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34
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35
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36 #variables to store the name of the R script file
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37 my $r_script;
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38
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39 # R script to implement the two-sample test on the motif frequencies in upstream flanking region
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40 #construct an R script file and save it in the same directory where the perl file is located
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41 $r_script = "non_pooled_t_test_two_samples.r";
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42
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43 open(Rcmd,">", $r_script) or die "Cannot open $r_script \n\n";
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44 print Rcmd "
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45 sampleTable1 <- read.table(\"$firstSampleInputFile\", header=FALSE);
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46 sample1 <- sampleTable1[, 1];
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47
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48 sampleTable2 <- read.table(\"$secondSampleInputFile\", header=FALSE);
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49 sample2 <- sampleTable2[, 1];
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50
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51 testSideStatus <- \"$testSidedness\";
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52 STEqualityStatus <- \"$standardDeviationEquality\";
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53
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54 #open the output a text file
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55 sink(file = \"$outputFile\");
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56
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57 #check if the t-test is two-sided
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58 if (testSideStatus == \"two-sided\"){
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59
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60 #check if the standard deviations are equal in both populations
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61 if (STEqualityStatus == \"equal\"){
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62 #two-sample t-test where standard deviations are assumed to be unequal, the test is two-sided
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63 testResult <- t.test(sample1, sample2, var.equal = TRUE);
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64 } else{
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65 #two-sample t-test where standard deviations are assumed to be unequal, the test is two-sided
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66 testResult <- t.test(sample1, sample2, var.equal = FALSE);
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67 }
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68 } else{ #the t-test is one sided
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69
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70 #check if the t-test is two-sided with m1 < m2
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71 if (testSideStatus == \"one-sided:_m1_less_than_m2\"){
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72
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73 #check if the standard deviations are equal in both populations
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74 if (STEqualityStatus == \"equal\"){
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75 #two-sample t-test where standard deviations are assumed to be unequal, the test is one-sided: Halt: m1 < m2
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76 testResult <- t.test(sample1, sample2, var.equal = TRUE, alternative = \"less\");
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77 } else{
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78 #two-sample t-test where standard deviations are assumed to be unequal, the test is one-sided: Halt: m1 < m2
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79 testResult <- t.test(sample1, sample2, var.equal = FALSE, alternative = \"less\");
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80 }
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81 } else{ #the t-test is one-sided with m1 > m2
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82 #check if the standard deviations are equal in both populations
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83 if (STEqualityStatus == \"equal\"){
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84 #two-sample t-test where standard deviations are assumed to be unequal, the test is one-sided: Halt: m1 < m2
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85 testResult <- t.test(sample1, sample2, var.equal = TRUE, alternative = \"greater\");
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86 } else{
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87 #two-sample t-test where standard deviations are assumed to be unequal, the test is one-sided: Halt: m1 < m2
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88 testResult <- t.test(sample1, sample2, var.equal = FALSE, alternative = \"greater\");
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89 }
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90 }
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91 }
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92
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93 #save the output of the t-test into the output text file
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94 testResult;
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95
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96 #close the output text file
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97 sink();
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98
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99 #eof" . "\n";
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100
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101 close Rcmd;
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102
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103 system("R --no-restore --no-save --no-readline < $r_script > $r_script.out");
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104
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105 #close the input and output files
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106 close(OUTPUT);
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107 close(INPUT2);
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108 close(INPUT1);
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109
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