Problem #1

This code will read your input file 1 line at a time, and filter out just the lines you require, without reading the whole file into memory at once. You would need to redirect the output to a file. 

use strict;
use warnings;

my $flag = 0;
while (<DATA>) {
    if (/^A id/) {
        print;
        $flag = 1;
    }
    print if $flag and /^M/
}

__DATA__
A class 1 1 1 1 1 1
A id 12 12 15 15 16 16 
B class 0 0 0 0 0 0 
B id 0 0 0 0 0 0 0 
C id 0 0 0 0 0 0 0 
M X1 1 2 2 2 2 2 
M X2 2 1 1 1 1 1 
M X3 1 2 2 2 2 2 
M X4 2 2 2 1 1 2 
M X5 1 1 1 1 1 1 
M X6 1 1 1 2 2 1 
M X7 1 1 1 1 1 1 
M X8 1 1 1 1 1 1 
M X9 1 1 1 1 1 1 
M X10 1 1 1 1 1 1 
M X11 1 2 1 1 1 1 
M X12 2 2 2 2 2 2 
M X13 2 1 2 2 2 2 
M X14 2 1 2 2 2 2 
M X15 1 2 1 1 1 1 
M X16 1 1 2 2 2 2 
M X17 1 2 2 2 2 2

[download]

Problem #2

I'm trying to understand your comparison requirements. Could you elaborate?

Update: Here's a guess... 

use strict;
use warnings;

while (<DATA>) {
    next if /^A id/;
    my ($x, $c1, $c2, @cols) = (split)[1..7];

    print "$x: col 12, 1st: $c1\n";
    for my $col (@cols) {
        if ($c1 == $col) {
            print "    matches\n";
        }
        else {
            print "    does not match\n";
        }
    }

    print "$x: col 12, 2nd: $c2\n";
    for my $col (@cols) {
        if ($c2 == $col) {
            print "    matches\n";
        }
        else {
            print "    does not match\n";
        }
    }
}

__DATA__
A id 12 12 15 15 16 16
M X1 1 2 2 2 2 2
M X2 2 1 1 1 1 1
M X3 1 2 2 2 2 2
M X4 2 2 2 1 1 2

[download]
Prints... 
X1: col 12, 1st: 1
    does not match
    does not match
    does not match
    does not match
X1: col 12, 2nd: 2
    matches
    matches
    matches
    matches
X2: col 12, 1st: 2
    does not match
    does not match
    does not match
    does not match
X2: col 12, 2nd: 1
    matches
    matches
    matches
    matches
X3: col 12, 1st: 1
    does not match
    does not match
    does not match
    does not match
X3: col 12, 2nd: 2
    matches
    matches
    matches
    matches
X4: col 12, 1st: 2
    matches
    does not match
    does not match
    matches
X4: col 12, 2nd: 2
    matches
    does not match
    does not match
    matches

[download]

In reply to Re: Column Comparison of a File in Perl by toolic
in thread Column Comparison of a File in Perl by snape

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