GWAS系列--从hmp格式基因型到 Structure 格式转

一个脚本，解决从基因型到运行 Structure 软件所需要的格式：

#!/usr/bin/perl -w
use strict;

die "Usage: perl $0 <infile.txt> STDOUT\n" if @ARGV < 1;
my %out;
my @genes;

open IN, $ARGV[0] || die $!;
chomp (my $header = <IN>);
my @samples = split /\t/, $header;
while(<IN>){
    chomp;
    my @a = split /\t/, $_;
    push @genes, $a[0];
    for (my $i=1;$i<@a;$i++){
        my @v = split //, $a[$i];
        $out{$samples[$i]}{$a[0]} = \@v;
    }
}
close IN;


my $out_first = join ("\t", "ID", sort @genes);
print "$out_first\n";

foreach my $sample ( sort keys %out){
    my ($out1, $out2);
    foreach my $k (sort keys $out{$sample}){
        
        my $left = $out{$sample}{$k}->[0];
        my $right = $out{$sample}{$k}->[1];
        $out1 .= "$left\t";
        $out2 .= "$right\t";
    }
    $out1 =~ s/N/-9/g;
    $out1 =~ s/\t$//g;
    $out2 =~ s/N/-9/g;
    $out2 =~ s/\t$//g;

    print "$sample\t$out1\n$sample\t$out2\n";

}
__END__

有问题讨论！