Hi Monks, I have a list of terms that need to be search for occurrneces in all files within a directory - basically I would like the same behaviour as unix grep. I have written some code but the section where I grep does not seem to work. 

my @ids =<IDLIST>;

my $dir = $opts{d};
chdir($dir) or die "$!";
opendir(DIR, ".") or die "Can't open $dir: $!";
my @files = grep {/fa$/}  readdir DIR;
close DIR;
foreach my $id (@ids) {
   foreach my $fasta (@files){
        local @ARGV = @files;
        print grep (/$id/,<>), "\n";
   }
}

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The reason I dont use unix grep is that I need to further post process the result.

I know each $id in @ids does occur in one of the files but in my code the result of print is always empty! - also, I would like to do this at the same speed as unix grep if possible. Any suggestions?

Thanks in advance, Chris.

In reply to faster way to grep by coldy

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