comment on

foreach my $line1(@array1)
{ 
    foreach my $line2(@array2)
        if
        {    $line1=~ /^$pattern/;
                        $line2=~ /^$pattern/;
                         $line1==$line2;
                        {  print $line1;    }
}
[download]

Your code has syntax error.

moreover eq is for comparing strings. == is for comparing numbers.

Adding code:

#!/usr/bin/perl
use strict;
use warnings;

open(FH, "<","./file1.txt") or die "Can't Open File1\n";
open(BH, "<","./file2.txt") or die "Can't Open File2\n";

my $pattern='^LOC_Os0[1-7]g[0-9]*.[0-9]\s';

while(my $line1 = <FH>)
{
        chomp($line1);
        #print "Line1:$line1\n";
        if( $line1=~ /$pattern/)
        {
                while(my $line2 = <BH>)
                {
                        chomp($line2);

                        if($line2 =~ /$pattern/)
                        {
                                if($line1 eq $line2)
                                {
                                        print "Matches: ". $line1;
                                }
                                else
                                {
                                        print "nothing to print\n";
                                }
                        }
                }
                seek(BH,0,0);
        }
}
close(FH);
close(BH);
[download]

file1.txt

LOC_Os01g01010.1 3017 : PAS 2993,3017 : AGTAAA AAATGGAGGAATTCTGCCA
LOC_Os01g01010.2 2218 : uORF 7,129 : ATG AAGAAGACGAGACGACGACTTCCCCACTA
+GGAAACACGACGGAGGCGGAGATGATC
[download]

file2.txt

LOC_Os01g01010.1 : PS51373 HIPIP High potential iron-sulfur proteins f
+amily profile. 2139 - 2208 AATGATTTATCATGTGAGGTGAAAGA-----AGAGCACCGGG
+TGAACAGTTACACAAGAA L=-1 GAAAGTCCAAAAGCA
LOC_Os01g01010.2 : PS00022 EGF_1 EGF-like domain signature 1. 298 - 30
+9 CtCccTtcGTtC L=(-1
LOC_Os01g01010.2 2218 : uORF 7,129 : ATG AAGAAGACGAGACGACGACTTCCCCACTA
+GGAAACACGACGGAGGCGGAGATGATC
[download]

All is well

In reply to Re: match pattern from two different file by vinoth.ree
in thread match pattern from two different file by Anonymous Monk

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