However, if your "tool" produces output that you want to capture and process, then you'll probably want to use backticks, eg:

$output_from_my_precompiled_tool = `/path/to/my/tool $file`;
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Thanks @Darren, will the code look like this? and also i want the output to be printed for respective files as different files in different directory

my $dir = '/path/to/dir';

# read only pd files:

opendir DIR, $dir or die "read dir $dir - $!";

my @pdb_files = grep /\.pdb/, readdir DIR;


closedir DIR;

foreach my $file (@pdb_files)

{

open( FH,"$dir\\$file")

while(<FH>) 

{

$output_from_my_precompiled_tool = `/path/to/my/tool $file`;

}
close(FH);

}
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Well, no. Probably not.

I'm not exactly clear whether you want to pass each entire file to your external tool, or whether you want to open each file and then pass it line by line. I guess probably the former. If that's the case, then perhaps this example will help.

$ echo 'some text' > 1.pdb
$ echo 'some more text' > 2.pdb
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Lets say for example your external tool is /bin/cat, and you want to cat each file and capture the output.

$ cat foo.pl
#!/usr/bin/perl
use strict;
use warnings;

my $dir = '.';
my $cat = '/bin/cat';
opendir DIR, $dir or die "Cannot open directory $dir:$!\n";
my @pdb_files = grep { -f $_ && $_ =~ /\.pdb$/ } readdir DIR;
closedir DIR;

for my $file (@pdb_files) {
    my $content = `$cat "$dir/$file"`;
    chomp $content;
    print "Content of $file is $content\n";

}
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$ perl foo.pl
Content of 1.pdb is some text
Content of 2.pdb is some more text
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That should be enough to get you going?