Hello all. I would like to do something akin to the join command using perl at the command line to make a hash and print lines where a value is in common between two files. The two files might have in common lets say... a gene identifier number or a CG number. These are always numbers and letter delimited somehow. What would the best way to do this at the command line be?

Original content restored above by GrandFather

I would like to accomplish this 
 use strict;


open (FILEHANDLE, "$ARGV[0]") || die("Could not open file 1 input file
+");
    my @file1 = <FILEHANDLE> ;
    close (FILEHANDLE);
    open (FILE2, "$ARGV[1]") || die ("Could not open file 2 input file
+");
    my @SAVI = <FILE2>;
close (FILE2);
   foreach my $line1 (@file1)
                    {
                        chomp ($line1);
                        (my $var1, my $var2) = split(/\t/,$line1);
                        
                        foreach my $line2 (@file2)
                         {
                             chomp($line2);
                             (my $Var1, my $Var2)= split(/\t/,$line2);
                             if ($var1=~m/$Var1/) {
                                print $line1 ."\t" . $line2  . "\n";
                               
                             }
                         }
                    }

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From the command line using maybe a hash or something so that its faster. Does anyone know how to do this sort of operation in a nice compact form? Basically just a way to see if a value in a column in one file appears in some form somewhere in a second file and printing the lines that are satisfy this.

In reply to Command Line Hash to print things in common between two files by ZWcarp

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