• What's ins?
• You use print with a format parameter, you probably meant printf?
• Also, DATA is not a format, it is a file handle.
• Moreover, what do you expect open(DATA,$in) to do? $in is a filehandle opened in the previous line, do you really want to use it as a file name?

First of all, you don't have to open DATA to read from it. Also, without looking it up or testing it, I'm not too sure what these two lines, in this combination, are supposed to do:

open my $in, "<", $infile;
open(DATA,$in);
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The next thing that strikes me as odd is the ins split /,\s*/ for <DATA>; line: where is ins defined? Is it imported from somewhere? Did you forget to include the relevant use ...; statement or the actual subroutine itself? Because as is, your code won't even run without an error message regarding this line.

Not to mention the fact that your code has use strict; and then uses an undeclared variable:

C:\Users\Lona\Desktop>perl x.pl
syntax error at x.pl line 15, near "ins split"
Global symbol "%group" requires explicit package name at x.pl line 16.
Execution of x.pl aborted due to compilation errors.

C:\Users\Lona\Desktop>
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Due to certain reasons I want to read in the input file in <DATA> format

Am I understanding you correctly that you want the code that reads from the filehandle to look like <DATA> instead of <$in>? Is that what you are trying to accomplish with open(DATA,$in);? If you could explain what your "certain reasons" are, that might help in finding a better solution.

Sorry guys, so here's everything Ive got.

#! /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]};
}
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Line no. 40 is printing out to console. But all those outputs I want in a user specified(while running the program) output file, apart from taking the input file also from command line , i.e. -->

perl program.pl input_file output_file
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The input file

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,
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To collect the file names from the command line, replace

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

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

chomp (my $outfile = shift);
open OUTPUT, '>', $outfile or die "Could not open $outfile\n";
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before the final for loop. Replace

  printf "%-4s: %20s,  %-8s %6s\n",
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with

  printf OUTPUT "%-4s: %20s,  %-8s %6s\n",
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1 Peter 4:10

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.)