Your code does not compile. Please do yourself a huge favor and  use warnings; and  use strict; at the start of every file. This is especially important for a novice Perler.

Even with strict and warnings, your code still has syntactic problems. The monks like to see working code, even if it does not do all (or even most) of what you want. Please see Short, Self-Contained, Correct Example.

Some syntactic thoughts:

• $b[$j] =s~/"//g; What is this statement supposed to do? Will it even compile?
• if ($j==1 && my @arr = grep { $_ =~ /\"1"$/ } @b); Will this compile?
• else Will this compile?

Some best-practices thoughts:

• my @a = <$fh1>; Is this supposed to read all lines from the file handle? Then why not name the variable  @lines or  @input_lines (since you want to transform them and then produce something like an  @output_lines array) instead?
• Similar objections apply to array names like  @arr and  @b
• if ($j==1 && my @arr = grep { $_ =~ /\"1"$/ } @b); Assuming this actually compiled, which  @arr in the script is referred to in the following  @arr = map{$_ = "P"} @arr; statement? (There are two  @arr arrays floating around in the script.)
• @arr = map {$b[$j] - 1} (1..$#b); A similar  @arr confusion attaches to this statement ...
• print @arr; ... and to this.

These comments are dashed off quickly. Although it may seem that way, I don't mean to be blunt or dismissive. I hope you will take them as food for thought.