$ 
$ cat input1a
"aphab"    "S1"    "S2"    "S3"
"a"    "A/A"    "A/A"    "A/A"
"b"    "A/G"    "A/G"    "A/A"
"c"    "A/A"    "G/G"    "A/A"
"d"    "G/G"    "A/G"    "A/G"
"e"    "A/G"    "G/G"    "A/G"
"f"     "A/A"    "G/G"    "A/G"
"g"    "A/A"    "G/G"    "G/G"
"h"    "A/A"    "G/G"    "G/G"
"I"     "A/A"    "G/G"    "G/G"
$ 
$ cat input1b
"aphab"    "S1"    "S2"    "S3"
"a"    "A/A"    "A/A"    "A/A"
"b"    "A/G"    "A/G"    "A/A"
"c"    "A/A"    "G/G"    "A/A"
"d"    "G/G"    "A/G"    "A/G"
"e"    "A/G"    "G/G"    "A/G"
"f"     "A/A"    "G/G"    "A/G"
"g"    "A/A"    "G/G"    "G/G"
"h"    "A/A"    "G/G"    "G/G"
"I"     "A/A"    "G/G"    "G/G"
$ 
$ cat input1c
"aphab"    "S1"    "S2"    "S3"
"a"    "A/A"    "A/A"    "A/A"
"b"    "A/G"    "A/G"    "A/A"
"c"    "A/A"    "G/G"    "A/A"
"d"    "G/G"    "A/G"    "A/G"
"e"    "A/G"    "G/G"    "A/G"
"f"     "A/A"    "G/G"    "A/G"
"g"    "A/A"    "G/G"    "G/G"
"h"    "A/A"    "G/G"    "G/G"
"I"     "A/A"    "G/G"    "G/G"
$ 
$ cat combine.pl
#!/usr/bin/perl -w

# check that at least 2 arguments are passed to this program
# exit with error code 1 otherwise
if ($#ARGV < 1) {
  print "Usage:   perl combine.pl <list of input files separated by space> input2\n";
  print "Example: perl combine.pl input1a input1b input1c input2\n";
  exit 1;
}

# now assign the list of "input1" file names to array @infile1
foreach (0..$#ARGV-1) {
  push @infile1, $ARGV[$_];
}
# set the variable $infile2 to the last argument i.e. the "input2" file
$infile2 = $ARGV[$#ARGV];

# define hashes - %chartonum, %numtochar and %mainhash
my %chartonum = qw(A/A 1 A/G 2 G/G 3);
my %numtochar = qw(1 A/A 2 A/G 3 G/G);
my %mainhash;

# first process all "input1" files i.e. all elements of the array @infile1
foreach $file1 (@infile1) {
  open(INFILE, $file1) or die "Can't open $file1: $!";
  while (<INFILE>) {
    chomp;
    s/"//g;
    s/[ ]+/ /g;
    if ($. == 1) {
      @x = split/ /;
    } else {
      @y = split/ /;
      foreach $i (1..$#y) {
        $mainhash{$x[$i].",".$chartonum{$y[$i]}}++;
      }
    }
  }
  close(INFILE) or die "Can't close $file1: $!";
}

# print the header
printf("%-12s%-12s%-12s%-12s%-12s%-s\n","\"ID\"","\"Label\"","\"StYPE\"","\"Ntype\"","\"Stype_No\"","\"log\"");
# now start processing the "input2" file
open(INFILE, $infile2) or die "Can't open $infile2: $!";
while (<INFILE>) {
  if ($. > 1) {
    chomp;
    s/"//g;
    s/[ ]+/ /g;
    # print $_,"\n";
    @z = split/ /;
    if (!defined $prev or $z[0] ne $prev) {$num = 1} else {$num++};
    $prev = $z[0];
    printf("%-12s%-12s%-12s%-12s%-12s%-s\n",
           "\"$z[0]\"",
           "\"$z[1]\"",
           defined $numtochar{$num} ? "\"$numtochar{$num}\"" : "\"NULL\"",
           exists $numtochar{$num} ? $num : "\"null\"",
           defined $mainhash{$z[0].",".$num} ? $mainhash{$z[0].",".$num} : "\"null\"", 
           $z[2]
          );
  }
}
close(INFILE) or die "Can't close $infile2: $!";

$ 
$ # Error checking - incorrect number of arguments
$ 
$ perl combine.pl
Usage:   perl combine.pl <list of input files separated by space> input2
Example: perl combine.pl input1a input1b input1c input2
$ 
$ perl combine.pl input1a
Usage:   perl combine.pl <list of input files separated by space> input2
Example: perl combine.pl input1a input1b input1c input2
$ 
$ perl combine.pl input2
Usage:   perl combine.pl <list of input files separated by space> input2
Example: perl combine.pl input1a input1b input1c input2
$ 
$ echo $?
1
$ 
$ # Successful run
$ 
$ perl combine.pl input1a input1b input1c input2
"ID"        "Label"     "StYPE"     "Ntype"     "Stype_No"  "log"
"S1"        "xxx"       "A/A"       1           18          2.8
"S1"        "xxx"       "A/G"       2           6           3
"S1"        "xxx"       "G/G"       3           3           4
"S2"        "yyy"       "A/A"       1           3           6.8
"S2"        "yyy"       "A/G"       2           6           7
"S2"        "yyy"       "G/G"       3           18          7.4
"S2"        "yyy"       "NULL"      "null"      "null"      8
"S3"        "zzz"       "A/A"       1           9           12
"S3"        "zzz"       "A/G"       2           9           14
"S3"        "zzz"       "G/G"       3           9           16
"S3"        "zzz"       "NULL"      "null"      "null"      18
"S3"        "zzz"       "NULL"      "null"      "null"      20
$ 
$ echo $?
0
$ 
$