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1 #!/usr/bin/perl
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2 # compares overlaps in the number of unique genes between two sets
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3
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4 use Getopt::Long;
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5
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6 #
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7 # command line arguments
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8 #
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9 $t1 = "";
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10 $t2 = "";
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11 $o = "";
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12 $of = 0;
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13 $n = 1;
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14
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15 $options = "Usage: ./Compare_Targets.pl <OPTIONS>
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16 -t1 .targets file 1 (EMBER output, required)
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17 -t2 .targets file 2 (EMBER output, required)
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18 -o output file (optional, if you want a gene list printed)
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19 output list prints all unique genes
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20 -of output type (default $of)
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21 0 - all shared targets
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22 1 - all targets in list 1 only
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23 2 - all targets in list 2 only
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24 3 - union of list 1 and 2
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25 -n compare gene names or probe ids (0 = ids, 1 = names, default $n)
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26 \n";
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27
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28 GetOptions('t1=s' => \$t1,
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29 't2=s' => \$t2,
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30 'o=s' => \$o,
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31 'of=i' => \$of,
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32 'n=i' => \$n
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33 ) || die "\n$options\n";
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34
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35 if( $t1 eq "" ){
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36 print "\nError: set a value for -t1\n\n$options\n";
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37 exit;
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38 }
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39 if( $t2 eq "" ){
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40 print "\nError: set a value for -t2\n\n$options\n";
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41 exit;
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42 }
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43 if( $of != 0 && $of != 1 && $of != 2 && $of != 3 ){
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44 print "\nError: set -of to be 0, 1, 2, or 3\n\n$options\n";
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45 exit;
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46 }
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47 if( $n != 0 && $n != 1 ){
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48 print "\nError: set -n to be 0 or 1\n\n$options\n";
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49 exit;
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50 }
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51
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52 #
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53 # read in gene list from each file
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54 #
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55 @list1 = &read_list( $t1 );
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56 @list2 = &read_list( $t2 );
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57
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58 printf("\nFound %i unique genes in %s, %i in %s\n", $#list1+1, $t1, $#list2+1, $t2);
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59
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60 #
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61 # compare lists and print out if desired
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62 #
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63 if( $o ne "" ){open(OUT,">$o");}
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64 $i = 0;
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65 $j = 0;
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66 $end1 = $#list1;
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67 $end2 = $#list2;
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68 $l1o = ();
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69 $l2o = ();
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70 $l12 = ();
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71 while( $i<= $end1 && $j<= $end2 ){
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72 if( $list1[$i] eq $list2[$j] ){
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73 if( $o ne "" && ($of == 0 || $of == 3) ){
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74 print OUT "$list1[$i]\n";
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75 }
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76 $l12++;
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77 $i++;
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78 $j++;
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79 }
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80 elsif( $list1[$i] lt $list2[$j] ){
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81 if( $o ne "" && ($of == 1 || $of == 3) ){
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82 print OUT "$list1[$i]\n";
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83 }
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84 $l1o++;
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85 $i++;
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86 }
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87 else{
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88 if( $o ne "" && ($of == 2 || $of == 3) ){
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89 print OUT "$list2[$j]\n";
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90 }
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91 $l2o++;
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92 $j++;
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93 }
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94 }
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95 if( $o ne "" ){close(OUT);}
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96 printf("\n%s only: %i\n%s only: %i\nshared: %i\n\n", $t1, $l1o, $t2, $l2o, $l12);
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97
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98
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99
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100
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101
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102 exit;
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103 ##############
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104 # read in gene list from .targets file and sort it, then only print those genes that are unique
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105 sub read_list{
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106 my @rval;
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107 my @sval;
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108 my @final;
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109
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110 @rval = ();
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111 open(IN,"$_[0]") || die "Error: can't open file $_[0]\n";
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112 while($line = <IN>){
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113 chomp($line);
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114 @parts = split(' ',$line);
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115 if( $parts[0] eq "GENE:" ){
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116 push(@rval, $parts[1+$n]);
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117 }
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118 if( $parts[0] eq "TGENE:" ){
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119 push(@rval, $parts[2+$n]);
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120 }
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121 }
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122 close(IN);
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123
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124 @sval = sort{ $a cmp $b } @rval;
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125
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126 @final = ();
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127 push(@final, @sval[0]);
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128 for($i=1; $i<= $#sval; $i++){
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129 if( $sval[$i] ne $sval[$i-1] ){
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130 push(@final, $sval[$i]);
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131 }
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132 }
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133
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134 return @final;
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135 }
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