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1 #!/usr/bin/perl
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2 # computes difference distances between motif models
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3
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4 if( $#ARGV != 1 ){
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5 print "Usage: ./Expression_Pattern_Distance.pl model1 model2\n";
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6 exit;
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7 }
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8
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9 @model1 = &read_model( $ARGV[0] );
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10 @model2 = &read_model( $ARGV[1] );
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11 if( $#model1 != $#model2 ){
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12 print "Error: model dimensions do not match\n";
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13 exit;
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14 }
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15
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16
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17 #
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18 # second distance: sum of absolute difference, divided by absolute sum
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19 # bounded between 0 and 1; equals 1 if all signs are different
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20 #
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21 $dist = 0;
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22 $denom = 0;
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23 for($i=0; $i< $classes; $i++){
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24 for($j=0; $j< $dims; $j++){
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25 if( $model1[$i][$j] ne "nan" && $model2[$i][$j] ne "nan" ){
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26 $dist+= abs($model1[$i][$j] - $model2[$i][$j]);
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27 $denom+= abs($model1[$i][$j]) + abs($model2[$i][$j]);
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28 }
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29 }
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30 }
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31 $dist/=$denom;
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32
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33 printf("%0.3f\n", $dist);
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34
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35
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36 exit;
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37
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38
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39
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40
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41 ################################
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42
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43 # function to read a motif model from file $_[0]
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44 sub read_model{
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45 $dims = 0;
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46 $classes = 0;
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47 open(IN,"$_[0]") || die "Error: can't open file $_[0]\n";
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48 @modpars = ();
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49 # burn the first two lines
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50 $line = <IN>;
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51 $line = <IN>;
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52 while( $line = <IN> ){
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53 chomp($line);
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54 @parts = split(' ',$line);
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55 if($parts[0] !~ /#/ ){
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56 @parts2 = ();
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57 for($i=1; $i<= $#parts; $i++){
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58 if( $parts[$i] ne "NA" ){
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59 push(@parts2, $parts[$i]);
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60 }
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61 else{
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62 push(@parts2, 0);
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63 }
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64 }
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65 push(@modpars, [@parts2] );
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66 $classes++;
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67 $dims = $#parts;
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68 }
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69 }
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70 close(IN);
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71 return @modpars;
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72 }
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73
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