#! /usr/bin/perl



#=======================Processing the input file=====================
+===#
print "Enter file name:\n";
chomp(my $file = <STDIN>);
open(DATA,$file) or die "failed opening file!!";
my %DEF = (
  I   => [qw( P Pl P.P P.Pl Pl.P Pl.Pl P.P.P P.P.Pl P.Pl.P P.Pl.Pl Pl.
+P.P Pl.P.Pl Pl.Pl.P Pl.Pl.Pl )],
  II  => [qw( E P.E Pl.E P.P.E P.Pl.E Pl.P.E Pl.Pl.E )],
  III => [qw( E.P E.Pl P.E.P P.E.Pl Pl.E.P Pl.E.Pl E.P.P E.P.Pl E.Pl.P
+ E.Pl.Pl )],
  IV  => [qw( E.E P.E.E Pl.E.E E.P.E E.Pl.E E.E.P E.E.Pl E.E.E )]
); # Hash table/dictionary for all the  groups
my @rank = map @$_, @DEF{qw(I II III IV)};
my %rank = map {$rank[$_-1] => $_} 1..@rank;
my @group = map {($_) x @{$DEF{$_}}} qw(I II III IV);
my %group = map {$rank[$_-1] => $group[$_-1]."_".$_} 1..@group;
sub rank { $rank{$a->[2]} <=> $rank{$b->[2]} }

my %T;

sub oh { map values %$_, @_ }
sub ab {
  my ($b, $a) = @_;
  [$b->[0], $a->[1], qq($a->[2].$b->[2]), qq($b->[3]<-$a->[3])]
}
sub xtend {
  my $a = shift;
  map {ab $_, $a} oh @{$T{$a->[0]}}{@_}
}
sub ins { $T{$_[3] //= $_[1]}{$_[2]}{$_[0]} = \@_ }

ins split /,\s*/ for <DATA>;
#ins split /,\s*/ for $filename;
ins @$_ for map {xtend $_, qw(P E Pl)} (oh oh oh \%T);
ins @$_ for map {xtend $_, qw(P E Pl)} (oh oh oh \%T);

for (sort {rank} grep {$_->[1] eq 'Q'} (oh oh oh \%T)) {
  printf "%-4s: %20s,  %-8s %6s\n",
      $_->[0], qq($_->[0]<-$_->[3]), $_->[2], $group{$_->[2]};
}
[download]

perl program.pl input_file output_file
[download]

input_file
M19,Q,P,
M31,M19,Pl,
M420,M31,E,
M421,M31,E,
M33,M31,E,
M438,M33,Pl,
M445,M33,E,
M437,M33,E,
M444,M33,E,
M73,M33,E,
M552,M73,Pl,
M553,M73,Pl,
M569,M73,E,
M549,M73,E,
M550,M73,E,
[download]

To collect the file names from the command line, replace

print "Enter file name:\n";
chomp(my $file = <STDIN>);
open(DATA,$file);
[download]

with

chomp(my $infile = shift);
open(DATA,$infile) or die "Could not open $infile\n";
[download]

Add

chomp (my $outfile = shift);
open OUTPUT, '>', $outfile or die "Could not open $outfile\n";
[download]

before the final for loop. Replace

  printf "%-4s: %20s,  %-8s %6s\n",
[download]

with

  printf OUTPUT "%-4s: %20s,  %-8s %6s\n",
[download]

1 Peter 4:10

You don't need to use chomp on values drawn from @ARGV. There's stuff in zing's code that doesn't make sense, but whatever the purpose may be, the basic template should be something like this:

die "Usage: $0  infile outfile\n" unless ( @ARGV == 2 );
my $infile = shift;
my $outfile = shift;

open( INPUT, '<', $infile ) or die "$infile: $!\n";
open( OUTPUT, '>', $outfile ) or die "$outfile: $!\n";

while (<INPUT>) {
    # do stuff with $_;
    # print something to OUTPUT
}
[download]

Regarding the use of @ARGV to get file names, see my reply above.

I have to rephrase choroba 's initial question: what is ins supposed to do? Also, what do you expect/intend to accomplish with the code (oh oh oh \%T)? (Is that supposed to be some sort of inside joke?)

If the input file contained just one line of data (e.g. "M19,Q,P,"), what would you want to see in the output file? (Be specific.)