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20
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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 use Switch;
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5 use Getopt::Long;
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6 use Bio::SeqIO;
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7
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8 my $usage = qq~Usage:$0 <args> [<opts>]
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9 where <args> are:
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10 -i, --input <input HAPMAP>
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11 -o, --output <output>
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12 -k, --kmin <K min. int>
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13 -m, --maxK <K max. int>
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14 -d, --directory <temporary directory>
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15 -p, --path <path to executables>
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16 ~;
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17 $usage .= "\n";
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18
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19 my ($input,$output,$kmin,$kmax,$directory,$path);
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20
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21
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22 GetOptions(
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23 "input=s" => \$input,
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24 "output=s" => \$output,
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25 "kmin=s" => \$kmin,
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26 "maxK=s" => \$kmax,
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27 "directory=s" => \$directory,
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28 "path=s" => \$path
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29 );
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30
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31
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32 die $usage
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33 if ( !$input || !$output || !$kmin || !$kmax || !$directory || !$path);
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34
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35 if ($kmin =~/^(\d+)\s*$/){
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36 $kmin = $1;
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37 }
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38 else{
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39 die "Error: kmin must be an integer\n";
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40 }
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41 if ($kmax =~/^(\d+)\s*$/){
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42 $kmax = $1;
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43 }
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44 else{
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45 die "Error: kmax must be an integer\n";
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46 }
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47
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48
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49 ######################
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50 # create map file
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51 ######################
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52 open(my $M,">$directory/input.map");
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53 open(my $H,$input);
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54 <$H>;
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55 while(<$H>)
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56 {
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57 my @infos = split(/\t/,$_);
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58 print $M $infos[2] . "\t" . $infos[0] . "\t" . "0" . "\t" . $infos[3] . "\n";
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59 }
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60 close($H);
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61 close($M);
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62
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63 ######################
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64 # create ped file
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65 ######################
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66 system("$path/transpose.awk $input >$directory/input.ped.2");
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67
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68 open(my $P,">$directory/input.ped");
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69 open(my $P2,"$directory/input.ped.2");
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70 my $n = 0;
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71 my $ind_num = 0;
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72 my @individus;
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73 while(<$P2>)
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74 {
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75 $n++;
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76 if ($n > 11)
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77 {
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78 my $line = $_;
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79 $line =~s/N/0/g;
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80 if (/^([^\s]+)\s+(.*)$/)
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81 {
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82 $ind_num++;
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83 my $ind = $1;
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84 push(@individus,$ind);
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85 my $genoyping_line = $2;
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86 print $P "$ind $ind_num 0 0 1 2";
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87 my @genotypes = split(/\s/,$genoyping_line);
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88 foreach my $genotype(@genotypes)
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89 {
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90 $genotype =~s/N/0/g;
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91 my @alleles = split("",$genotype);
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92 print $P " " . join(" ",@alleles);
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93 }
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94
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95 print $P "\n";
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96 }
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97 }
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98 }
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99 close($P2);
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100 close($P);
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101
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102 unlink("$directory/input.ped.2");
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103
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104 system("plink --file $directory/input --out $directory/out --make-bed --noweb >>$directory/plink.log 2>&1");
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105
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106
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107 ###################################
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108 # launch admixture for different K
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109 ###################################
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110 my %errors;
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111 for (my $k = $kmin; $k <= $kmax; $k++)
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112 {
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113 system("admixture --cv $directory/out.bed $k >>$directory/log.$k 2>&1");
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114 my $cv_error_line = `grep -h CV $directory/log.$k`;
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115 if ($cv_error_line =~/: (\d+\.*\d*)$/)
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116 {
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117 $errors{$1} = $k;
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118 }
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119 system("cat $directory/log.$k >>$directory/logs");
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120 system("echo '\n\n====================================\n\n' >>$directory/logs");
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121 system("cat out.$k.Q >>$directory/outputs.Q");
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122 system("echo '\n\n====================================\n\n' >>$directory/outputs.Q");
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123 system("cat out.$k.P >>$directory/outputs.P");
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124 system("echo '\n\n====================================\n\n' >>$directory/outputs.P");
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125 }
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126
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127 my @sorted_errors = sort {$a<=>$b} keys(%errors);
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128 my $best_K = $errors{@sorted_errors[0]};
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129
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130
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131 #system("cp -rf out.$best_K.Q $directory/output");
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132
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133 open(BEST1,"out.$best_K.Q");
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134 open(BEST2,">$directory/output");
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135 print BEST2 "<Covariate>\n";
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136 print BEST2 "<Trait>";
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137 for (my $j=1;$j<=$best_K;$j++)
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138 {
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139 print BEST2 " Q" . $j;
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140 }
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141 print BEST2 "\n";
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142 my $i = 0;
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143 while(<BEST1>)
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144 {
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145 my $line = $_;
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146 $line =~s/ /\t/g;
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147 my $ind = $individus[$i];
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148 print BEST2 "$ind ";
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149 print BEST2 $line;
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150 $i++;
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151 }
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152 close(BEST1);
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153 close(BEST2);
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154
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155 system("cp -rf $directory/log.$best_K $directory/log");
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156
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157
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158
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159
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