ok. Please consider again the input files, with both candidates, for E and M as well. File 1 
chr7    151046672
chr7    151047369
chr3    127680920
chr3    127680920

[download]
File 2 
chr1    66953622    66953654
chr1    67200451    67200472
chr1    67200475    67200478
chr1    67058869    67058880
chr1    67058881    67058885
chr7    151046672    127680920
chr7    151047369    127680920
chr3    127680920    151046672
chr3    127680920    151047369

[download]
Code for now. 
#!/usr/bin/perl
use warnings; 
use strict;
use Data::Dumper;

my $file1 = $ARGV[0];
open($infile1,$file1);
my $file2 = $ARGV[1];
open($infile2,$file2);

my %file2_hash;

while (my $line = <$infile1>)
{
   chomp $line;  #so that output with E or M can be on same line
   next if $line =~ /^\s*$/;   #skip blank lines (a common infile goof
+)
   
   my ($chr, $val1, $val2) = split /\s+/,$line;
}
close $infile1;

while (my $line = <$infile2>)
{
chomp $line;   
 next if $line =~ /^\s*$/;   #skip blank lines (a common infile goof)
   
   my ($key, $value1, $value2) = split /\s+/, $line; # use better "nam
+es" I have
                                           # no idea of what a chr col
   $file2_hash{"$key:$value1:$value2"} = 1;

  # file handle closure is optional, but I'd do it.

###  process each line in file2:
###  If a line "matches" with any line in file1, then "E", else "M"
###  I don't know that these numbers mean, come up with better comment

close $infile2;

   if (exists $file2_hash{"$chr:$val1:$val2"})
   {
      print "$line\tE\n";  # match exists with file 1   
}
   else
   {
   print "$line\tM\n";  # match does NOT exist with file 1
   
}

}

[download]
Its not working, Since I want to print the output with respect to my file 1. If you can help with. I Know there is some error in 'If' statement. I could note understand that..

In reply to Re^6: compare two files on the basis of Two IDs by genome
in thread compare two files on the basis of Two IDs by genome

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