I have some broblem about merging two files. this is my perl code which is not completed. $filename = "delete.txt"; unless ( -e $filename ) { print "The file $filename does not seem to exist \n"; exit; } print "\nThe file $filename exist and will be uploaded.\n"; unless ( open(FILEA , $filename)) { print "Can not open $filename \n"; exit; } my @readdata = <FILEA>; close FILEA; $filenameB = "delete2.txt"; unless ( -e $filenameB ) { print "The file $filenameB does not seem to exist \n"; exit; } print "\nThe file $filenameB exist and will be uploaded.\n"; unless ( open(FILEB , $filenameB)) { print "Can not open $filenameB \n"; exit; } my @readdataB = <FILEB>; close FILEB; #---extracting term from the first array my $linenum = @readdata; my $currline = 0; for($currline = 0; $currline < $linenum; $currline++) { my @splitdataA = split(" ", $readdata[$currline]); my $geneA = $splitdataA[2]; push (@exgenesA, $geneA); } my $linenumB = @readdataB; my $currlineB = 0; for($currlineB = 0; $currlineB < $linenumB; $currlineB++) { my @splitdataB = split(" ", $readdataB[$currlineB]); my $geneB = $splitdataB[1]; push (@exgenesB, $geneB); } @union = @isect = (); %union = %isect = (); foreach $e(@exgenesB) { $union{$e} = 1; } foreach $e(@exgenesA) { if ($union{$e}) { $isect{$e} = 1; } $union{$e} =1; } @union = keys %union; @isect = keys %isect; print join (",", sort @isect); exit; -------------------- input file (delete.txt) cd A1 B1 0.1 cd A2 B2 0.3 cd A3 B4 0.2 cd A5 B3 0.2 cd A6 B3 0.2 --------------------------- input file (delete2.txt) ab B1 A1 0.2 ab B2 A2 0.3 ab B3 A4 0.2 ab B5 A3 0.2 --------------------------- I tried search for pair of matching data the results should be Output : A1 B1 0.1 B1 A1 0.2 A2 B2 0.3 B2 A2 0.3 A3 B3 0.2 B3 A4 0.2 --------------------------- But in my code, i can only get intersec between them that are B1,B2 and B3. Could you please suggest me about extracting output like as over output. Thank you so much.

I tried to do my code to search matching pair in two files,shown like this : open(IF1, "data1.txt") or die "Error opening data file: $!\n"; my @a; while (<IF1>) { chomp; my @fields=split; for(my $j=0;$j<@fields;$j++){ push (@a,@fields[$j]); } } close(IF1); open(IF2, "data2.txt") or die "Error opening data file: $!\n"; my @b; while (<IF2>) { chomp; my @fields=split; for(my $j=0;$j<@fields;$j++){ push (@b,@fields[$j]); } } close(IF2); my $count = 0; for (my $i = 0; $i <8; $i++) { for (my $t = 0; $t <8; $t++) { # 8 mean total number of column, $i mean row, 1 and 2 mean position of column if ((@a[8*$i+1] eq @b[8*$t+2])and(@a[8*$i+2] eq @b[8*$t+1])) { $count++; for (my $k=1; $k<8; $k++) { my @c = push(@c,@a[(8*$i)+$k]); } for (my $k=1; $k<8; $k++) { my @c = push(@c,@b[(8*$t)+$k]); } } } } print @c; --------- data1.txt cc A1 B1 7e-14 149 33 74.3 181 cc A2 B3 5e-13 72 45 71.6 174 cc A3 B5 1e-11 152 30 64.7 156 cc A4 B6 1e-10 175 26 63.5 153 cc A5 B7 5e-10 95 33 62.8 151 --------- data2.txt aa B1 A1 4e-13 207 23 56.6 135 aa B2 A1 5e-13 207 23 56.6 135 aa B3 A2 6e-13 72 45 71.6 174 aa B4 A3 7e-12 163 31 69.3 168 aa B5 A3 8e-11 152 30 64.7 156 aa B6 A3 9e-10 175 26 63.5 153 -------- The result showed like this : A1 B1 7e-14 149 33.5570469798658 74.3 181 B1 A1 4e-13 207 23.6714975845411 56.6 135 A1 B1 6e-14 149 33.5570469798658 74.3 181 B1 A1 4e-13 207 23.6714975845411 56.6 135 A2 B3 5e-13 72 45.8333333333333 71.6 174 B3 A2 6e-13 72 45.8333333333333 71.6 174 A3 B5 1e-11 152 30.9210526315789 64.7 156 B5 A3 8e-11 152 30.9210526315789 64.7 156 ----------- I have some problem about lines. I want lines like this in one time of matching : A1 B1 7e-14 149 33 74.3 181 B1 A1 4e-13 207 23 56.6 135 A2 B3 5e-13 72 45 71.6 174 B3 A2 6e-13 72 45 71.6 174 A3 B5 1e-11 152 30 64.7 156 B5 A3 8e-11 152 30 64.7 156 you can see matching pair like that. Please suggest me about code or output like that. Thank you so much. Now I feel my code is very slow for running data which have hundred thousand lines.