perl/etc/WoodyMiaoLin/Tiger/generate_input_step2.pl

   1 #!/usr/bin/perl
   2 use strict;
   3 use warnings;
   4
   5 open I, "<", "scaffold75_1458SNP.16.gt";
   6 open O, ">", "scaffold75_1458.16.inp";
   7
   8 my $id = <I>;
   9 chomp $id;
  10 my @id = split /\t/, $id;
  11 my (@pos, @gt);
  12 while (<I>) {
  13         chomp;
  14         my @a = split /\t/;
  15         push @pos, $a[1];
  16         foreach (2 .. 17) {
  17                 my @b = split /\//, $a[$_];
  18                 $gt[$_][0] .= $b[0];
  19                 $gt[$_][1] .= $b[1];
  20         }
  21 }
  22 close I;
  23
  24 my $num_indi = @id-2;
  25 my $num_loci = @pos;
  26 print O "$num_indi\n";
  27 print O "$num_loci\n";
  28 print O (join " ", "P", @pos), "\n";
  29 print O ("S" x $num_loci), "\n";
  30 foreach (2 .. 17) {
  31         print O $id[$_], "\n";
  32         print O $gt[$_][0], "\n";
  33         print O $gt[$_][1], "\n";
  34 }
  35 close O;