perl/etc/WoodyMiaoLin/Tiger/generate_input_step1.pl

   1 #!/usr/bin/perl
   2 use strict;
   3 use warnings;
   4
   5 open I1, "<", "scaffold75SNP.18.gt";
   6 open I2, "<", "scaffold1458SNP.18.gt";
   7 open O, ">", "scaffold75_1458SNP.16.gt";
   8
   9 print O "#Scaffold\tPosition\tJHH001\tGZXJ03\tGZXJ05\tGZXJ26\tGZXJ27\tGZXJ28\tGZXJ29\tGZXJ30\tGZXJ33\tBHX011\tBHX019\tGZXJ04\tGZXJ06\tGZXJ31\tGZXJ32\tGZXJ38\n";
  10
  11 while (<I1>) {
  12         chomp;
  13         my @a = split /\t/;
  14         foreach (4 .. 21) {
  15                 my @b = split /\//, $a[$_];
  16                 $a[$_] = "$a[2]/$a[2]" if (($b[0] eq 0) and ($b[1] eq 0));
  17                 $a[$_] = "$a[3]/$a[3]" if (($b[0] eq 1) and ($b[1] eq 1));
  18                 $a[$_] = "$a[2]/$a[3]" if (($b[0] eq 0) and ($b[1] eq 1));
  19                 $a[$_] = "$a[3]/$a[2]" if (($b[0] eq 1) and ($b[1] eq 0));
  20         }
  21         splice @a, -3, 2;
  22         splice @a, 2, 2;
  23         print O (join "\t", @a), "\n";
  24 }
  25
  26 while (<I2>) {
  27         chomp;
  28         my @a = split /\t/;
  29         $a[1] += 5658748;
  30         foreach (4 .. 21) {
  31                 my @b = split /\//, $a[$_];
  32                 $a[$_] = "$a[2]/$a[2]" if (($b[0] eq 0) and ($b[1] eq 0));
  33                 $a[$_] = "$a[3]/$a[3]" if (($b[0] eq 1) and ($b[1] eq 1));
  34                 $a[$_] = "$a[2]/$a[3]" if (($b[0] eq 0) and ($b[1] eq 1));
  35                 $a[$_] = "$a[3]/$a[2]" if (($b[0] eq 1) and ($b[1] eq 0));
  36         }
  37         splice @a, -3, 2;
  38         splice @a, 2, 2;
  39         print O (join "\t", @a), "\n";
  40 }
  41
  42 close I1;
  43 close I2;
  44 close O;