open INFILE, "$ARGV[0]"; @aTryptic = ; close INFILE; shift @aTryptic; for ($i=0;$i<@aTryptic;$i++) { $accSeq = SplitFields($aTryptic[$i], 'split'); $aTryptic[$i] =~ s/\r\n$/\n/g; chomp $aTryptic[$i]; $hTryptic{$accSeq} = $aTryptic[$i]; $aTryptic[$i] = $accSeq; } open INFILE, "$ARGV[1]"; @aSemiTryptic = ; close INFILE; shift @aSemiTryptic; for ($i=0;$i<@aSemiTryptic;$i++) { $accSeq = SplitFields($aSemiTryptic[$i], 'split'); $aSemiTryptic[$i] =~ s/\r\n$/\n/g; chomp $aSemiTryptic[$i]; $hSemiTryptic{$accSeq} = $aSemiTryptic[$i]; $aSemiTryptic[$i] = $accSeq; } #### foreach $one (@arrayA) { chomp $one; $found = 0; foreach $two (@arrayB) { chomp $two; if ($one eq $two) { print "$hashB{$two}"; $found = 1; last; } } if ($found == 0) { print "$hashA{$one}"; } }