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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 $PLINK_EXE= "plink";
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9
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10 my $usage = qq~Usage:$0 <args> [<opts>]
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11 where <args> are:
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12 -i, --in <input>
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13 -o, --out <output>
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14 ~;
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15 $usage .= "\n";
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16
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17 my ($in,$out);
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18
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19
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20 GetOptions(
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21 "in=s" => \$in,
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22 "out=s" => \$out
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23 );
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24
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25 die $usage
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26 if ( !$in || !$out);
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27
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28
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29 my $plink_command = $PLINK_EXE . " --file $in --noweb --cluster --matrix --mds-plot 2 --out $out >>$in.plink.log 2>&1";
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30 system($plink_command);
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31
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32 my $awk_cmd = "awk \{\'print \$1\'\} $in.ped";
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33 my $inds = `$awk_cmd`;
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34 my @individuals = split("\n",$inds);
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35
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36 my %populations;
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37 if (-e "$in.individual_info.txt")
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38 {
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39 open(my $I,"$in.individual_info.txt");
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40 while(<$I>)
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41 {
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42 my $line = $_;
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43 $line =~s/\n//g;
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44 $line =~s/\r//g;
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45 my ($ind,$pop) = split(/;/,$line);
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46 $populations{$ind} = $pop;
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47 }
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48 close($I);
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49 }
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50
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51 open(my $OUT,">$out.mds_plot.txt");
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52 my $go = 0;
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53 open(my $O,"$out.mds");
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54 while(<$O>)
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55 {
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56 if ($go)
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57 {
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58 my $line = $_;
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59 $line =~s/\n//g;
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60 $line =~s/\r//g;
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61 my @i = split(/\s+/,$line);
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62 if ($line =~/^ /)
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63 {
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64 my $ind = $i[1];
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65 my $pop = "Pop1";
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66 if ($populations{$ind})
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67 {
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68 $pop = $populations{$ind};
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69 }
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70 print $OUT "$pop $ind ".$i[4]." ".$i[5]."\n";
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71 }
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72 if ($line =~/^\w/)
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73 {
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74 my $ind = $i[0];
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75 my $pop = "Pop1";
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76 if ($populations{$ind})
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77 {
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78 $pop = $populations{$ind};
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79 }
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80 print $OUT "$pop $ind ".$i[3]." ".$i[4]."\n";
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81 }
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82
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83 }
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84 if (/C1/){$go = 1;}
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85 }
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86 close($O);
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87 close($OUT);
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88
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89
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90 my $j = 0;
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91 open(my $IBS,">$out.ibs_matrix.txt");
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92 print $IBS "Individuals " . join("\t",@individuals)."\n";
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93 open(my $O2,"$out.mibs");
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94 while(<$O2>)
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95 {
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96 my $line = $_;
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97 $line =~s/\n//g;
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98 $line =~s/\r//g;
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99 my @i = split(/\s+/,$line);
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100 print $IBS $individuals[$j]. " ". join("\t",@i)."\n";
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101 $j++;
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102 }
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103 close($O2);
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104 close($IBS);
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105
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106
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107
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108
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109
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110
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