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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$ 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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Sorry @Darren the program doesn't seems to work because its asking for two input files first input file is the exterior script(written already)and the second input is the PDB files. So,i think incorporating a function which calls the script file first followed by the PDB files will help. So, could you please tell me how to do this?

I'm sorry, but I'm a bit lost.

I understand that English might not be your first language, but you're not doing a very good job of explaining what you need (no offense intended).

This is what I understand from your posts so far:

• You have a number of files with a .pdb extension
• You have a tool that processes these files in some way
• You want to use perl to feed these files to this tool
Now, assuming that the above is correct - I have a couple of questions for you.
Firstly, how do these files need to be passed to your external tool? Do you need to a) just pass the name and location of the file, or b) open the file within perl and then pass it line by line?

And secondly, does this external tool produce any output? And if it does, what should be done with that output?

Perhaps if you can describe as best you can the steps you would take if you were going to process one of these files manually (from start to finish), then that might help me to understand a bit better what it is you need.

will the code look like this? after embedding the external script ?

#!/usr/bin/perl

use strict;
use warnings;


my $dir = '.';

#for embeding the mcsearch percompile version
my $mcsearch = '/bin/mcsearch';

#to read the PDB files from the directory
opendir DIR, $dir or die "Cannot open directory $dir:$!\n";

my @pdb_files = grep { -f $_ && $_ =~ /\.pdb$/ } readdir DIR;

closedir DIR;

print "Enter the script file";
$a=<>;

open(IN,$a) or die;


#giving each file as a input to mcsearch
for my $file (@pdb_files)

 {
while(<>)

{
    my $content = `$mcsearch "$dir/$file"`;

    chomp $content;

    print "Content of $file is $content\n";

}
}
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http://www.major.iric.ca/MajorLabEn/MC-Tools_files/MC-Annotate.zip here is the tool, i want to embed this tool and give the inputs to the tool, the web version of this tool looks like http://www.major.iric.ca/MC-Search/

So looking at the web version i was trying to provide two inputs