try this
#!/usr/bin/perl
use warnings;
use strict;
my %bow1 = ();
my $file1 = shift;
open (FILE1, "$file1")or die "could not open FILE1:$file1; # Open firs
+t file
while (<FILE1>) {
my ($ID1, undef, undef, undef, $Seq1) = split;
$bow1{$ID1} = $ID1; # your id is the key and can be got again
}
close FILE1;
my $file2 = shift;
open (FILE2, "$file2")or die "could not open FILE2:$file2"; # Open sec
+ond file
while (<FILE2>) {
my ($ID2, undef, undef, undef, $Seq2) = split;
if(defined($bow1{$ID2})){#IDs Match
if($bow1{$ID2} eq $Seq2){
#both match so remove from the hash to avoid looking fo
+r a correct one later
delete $bow1{$ID2};
}else{
#id's dont match
print "IDs exist but dont match ID:$ID2:Seq1:$bow1{$ID2}:Seq2:$
+Seq2:\n";
}
}else{
#id not in list 1
print "ID only in file 2 ID:$ID2:$Seq1\n"
}
}
close FILE2
#run through any remaing list one items that werent matched
while((my $key,my $value) = each %bow1){
print "ID only in file 1 ID:$key:Seq:$value:\n";
}