You've completely missed the point of using a hash. You do not need to iterate every key to see if it contains the value you want, you just use the value as the key.
Try this. It should (untested) produce the same output and run much, much (much:), faster: #!/usr/bin/perl -w
# perl.ID.match.pl
use strict; use warnings;
open(KEY, "<chr1.coverage.txt") or die "error reading file";
my %Chr;
my (@Key,@line);
while (my $key = <KEY>) {
chomp $key;
@Key=split("\t",$key);
$Chr{$Key[0]} = undef;
}
open(FULL, "<chr1.txt") or die "error reading file";
open(OUT, ">chr1.match.txt") or die "error reading file";
while (my $line=<FULL>) {
chomp $line;
@line=split("\t",$line);
if( exists $Chr{ $line[0] } ) {
print OUT "$line\n";
}
}
close KEY;
close FULL;
close OUT;
exit;
Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
"Science is about questioning the status quo. Questioning authority".
In the absence of evidence, opinion is indistinguishable from prejudice.
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