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12
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1 use strict;
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2
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3
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4 my $inputfile = $ARGV[0];
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5 my $usemaxent = 1;
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6
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7 my $modelpath = "/home/sharp-galaxy.orig/tools/maxentscan";
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8 my %me2x5 = &makescorematrix($modelpath.'me2x5');
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9 my %seq = &makesequencematrix($modelpath.'splicemodels/splice5sequences');
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10
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11 my %bgd;
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12 $bgd{'A'} = 0.27;
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13 $bgd{'C'} = 0.23;
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14 $bgd{'G'} = 0.23;
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15 $bgd{'T'} = 0.27;
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16
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17
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18
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19 open (FILE,"<$inputfile") || die "can't open!\n";
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20
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21 while(<FILE>) {
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22 chomp;
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23 if (/^\s*$/) { #discard blank lines;
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24 next;
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25 }
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26 elsif (/^>/) { #discard comment lines;
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27 print $_."\t";
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28 next;
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29 }
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30 elsif (/[NQWERYUIOPLKJHFDSZXVBM]/) {
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31 next;
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32 }
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33 else {
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34 $_ =~ s/\cM//g; #gets rid of carriage return
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35 my $str = $_;
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36 print $str."\t";
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37 $str = uc($str);
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38 if ($usemaxent) {
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39 print sprintf("%.2f",&log2(&scoreconsensus($str)*$me2x5{$seq{&getrest($str)}}))."\n";
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40 }
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41 }
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42 }
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43
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44
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45 sub makesequencematrix{
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46 my $file = shift;
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47 my %matrix;my $n=0;
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48 open(SCOREF, $file) || die "Can't open $file!\n";
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49 while(<SCOREF>) {
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50 chomp;
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51 $_=~ s/\s//;
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52 $matrix{$_} = $n;
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53 $n++;
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54 }
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55 close(SCOREF);
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56 return %matrix;
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57 }
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58 sub makescorematrix{
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59 my $file = shift;
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60 my %matrix;my $n=0;
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61 open(SCOREF, $file) || die "Can't open $file!\n";
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62 while(<SCOREF>) {
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63 chomp;
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64 $_=~ s/\s//;
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65 $matrix{$n} = $_;
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66 $n++;
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67 }
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68 close(SCOREF);
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69 return %matrix;
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70 }
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71
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72 sub getrest{
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73 my $seq = shift;
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74 my @seqa = split(//,uc($seq));
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75 return $seqa[0].$seqa[1].$seqa[2].$seqa[5].$seqa[6].$seqa[7].$seqa[8];
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76 }
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77 sub scoreconsensus{
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78 my $seq = shift;
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79 my @seqa = split(//,uc($seq));
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80 my %bgd;
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81 $bgd{'A'} = 0.27;
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82 $bgd{'C'} = 0.23;
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83 $bgd{'G'} = 0.23;
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84 $bgd{'T'} = 0.27;
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85 my %cons1;
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86 $cons1{'A'} = 0.004;
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87 $cons1{'C'} = 0.0032;
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88 $cons1{'G'} = 0.9896;
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89 $cons1{'T'} = 0.0032;
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90 my %cons2;
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91 $cons2{'A'} = 0.0034;
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92 $cons2{'C'} = 0.0039;
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93 $cons2{'G'} = 0.0042;
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94 $cons2{'T'} = 0.9884;
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95 my $addscore = $cons1{$seqa[3]}*$cons2{$seqa[4]}/($bgd{$seqa[3]}*$bgd{$seqa[4]});
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96 return $addscore;
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97 }
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98
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99 sub log2{
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100 my ($val) = @_;
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101 return log($val)/log(2);
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102 }
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