open(FILE1, $ARGV[0]); while($line = ) { chomp($line); @words = split(/\t/, $line); $hash1{$words[0]} = $words[1]; } close(FILE1); open(FILE3, ">$ARGV[2]"); while (($key, $value) = each(%hash1)){ print FILE3 $key."\t".$value."\n"; } print "\n"; open(FILE1, $ARGV[1]); %hash2 = map { chomp; split /\t/ } ; close(FILE1); while (($key, $value) = each(%hash2)){ print FILE3 $key."\t".$value."\n"; } print "\n"; #### __DATA1__ trip value1 value2 ATG adsad dsf CTG 23432 2342 TTA 24312 144 CTT 452 5fw ATA rff sgsh __DATA2__ trip value3 ATG asdas CCG asdadd TTA 24 CAT 45 __OUTPUT / DESIRED__ trip value1 value2 value3 ATG adsad dsf asdas TTA 24312 144 24