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9
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1 #!/usr/bin/perl
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2
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3 use strict;
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4
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5 use Getopt::Long;
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6
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7 my $usage = qq~Usage:$0 <args> [<opts>]
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8 where <args> are:
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9 -h, --hapmap <Hapmap input file>
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10 -m, --map <Map output file>
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11 -g, --geno <Genotype output file>
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12 -p, --path <Path for transpose executable>
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13 ~;
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14 $usage .= "\n";
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15
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16 my ($hapmap,$map,$geno,$path);
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17
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18
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19 GetOptions(
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20 "geno=s" => \$geno,
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21 "map=s" => \$map,
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22 "hapmap=s" => \$hapmap,
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23 "path=s" => \$path,
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24 );
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25
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26
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27 die $usage
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28 if ( !$geno || !$map || !$hapmap || !$path);
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29
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30 my $TRANSPOSE_EXE = "$path/transpose.awk";
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31
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32 my @snps;
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33 my %chrom_pos;
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34 my $num_line = 0;
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35 open(my $O,">geno_transposed");
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36 open(my $H,$hapmap);
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37 while(<$H>)
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38 {
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39 $num_line++;
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40 my $line = $_;
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41 chomp($line);
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42 $line =~s/\r//g;
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43 $line =~s/\n//g;
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44 my @infos = split(/\t/,$line);
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45 if ($num_line == 1)
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46 {
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47 print $O "Ind_id";
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48 for (my $i = 11; $i <= $#infos; $i++)
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49 {
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50 my $individual = $infos[$i];
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51 print $O " " . $individual;
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52 }
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53 print $O "\n";
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54 }
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55 elsif ($num_line > 1)
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56 {
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57 my $snp = $infos[0];
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58 my $variation = $infos[1];
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59 my %scores;
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60 if ($variation =~/(\w)\/(\w)/)
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61 {
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62 my $allele1 = $1;
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63 my $allele2 = $2;
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64 $scores{$allele1} = 0;
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65 $scores{$allele2} = 1;
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66 }
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67 my $chrom = $infos[2];
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68 my $pos = $infos[3];
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69 $chrom_pos{$snp}{"chrom"} = $chrom;
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70 $chrom_pos{$snp}{"pos"} = $pos;
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71 push(@snps,$snp);
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72 print $O "$snp";
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73 for (my $i = 11; $i <= $#infos; $i++)
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74 {
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75 my $genotype = $infos[$i];
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76 my @alleles = split("",$genotype);
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77 if ($genotype ne "NN")
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78 {
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79 my $score = $scores{$alleles[0]} + $scores{$alleles[1]};
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80 print $O " $score";
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81 }
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82 else
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83 {
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84 print $O " NA";
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85 }
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86 }
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87 print $O "\n";
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88 }
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89 }
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90 close($H);
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91 close($O);
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92
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93 open(my $M,">$map");
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94 print $M "SNP Chr Pos\n";
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95 foreach my $snp(@snps)
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96 {
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97 print $M "$snp " . $chrom_pos{$snp}{"chrom"} . " ". $chrom_pos{$snp}{"pos"} . "\n";
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98 }
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99 close($M);
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100
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101 system("$TRANSPOSE_EXE geno_transposed >geno_transposed2");
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102
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103 open(my $F,">$geno");
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104 open(my $G,"geno_transposed2");
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105 while(<$G>)
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106 {
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107 my $line = $_;
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108 $line =~s/ /\t/g;
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109 print $F $line;
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110 }
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111 close($G);
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112 close($F);
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113
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114 unlink("geno_transposed");
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115 unlink("geno_transposed2");
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116
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117
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