use strict;
use warnings;
use Carp qw(croak);
{
    my $input_file = "input_file.txt";
    my @lines = slurp($input_file);
    for my $line (@lines){
        my ($filename, $ligand) = split(/\t/, $line);
        open(FILE, '<', $filename) or die "Cannot open file: $!";
        while (my $line = <FILE>) {
            print $line if $line =~ /$ligand/;
        }
        close(FILE);
    }   
}

##Slurps a file into a list
sub slurp {
    my ($file) = @_;
    my (@data, @data_chomped);
    open IN, "<", $file or croak "can't open $file\n";
    @data = <IN>;
    for my $line (@data){
        chomp($line);
        push (@data_chomped, $line);
    }
    close IN;
    return (@data_chomped);
}
[download]

file1.txt       MC9
file2.txt       ASH
[download]

Can I ask you for little more help? The program helped me so much. Thanks for that. Now I need to modify it a bit more. I tried myself but got stuck at one point. Can u help me out?

 
so now I don't want to print the line containing ligand name , rather now i want to count no of lines and want to count amongst those lines, the lines containing H as a 1st character of each row. I successfully counted the lines by using following code

# changed the code from line 10 of above written code
while (my $line= <FILE>
{ $ count=0;
if $line=~/$ligand/;
{
$count++;}
}
Print"total no of interaction are $count";
}close (FILE);
}
[download]

 this counts only no of lines. Now, I want while the program is reading code line by line it should check the first character and if it is H the it should count that line and put the count in another variable say count2 or something.
 
 Please help 

I made this program, but it is giving so many errors. Can you help me in debugging it.

use strict;
use warnings;
use Carp qw(croak);
{
    my $input_file = "input_file.txt";
    my @lines = slurp($input_file);
    for my $line (@lines){
        my ($filename, $ligand) = split(/\t/, $line);
        open(FILE, '<', $filename) or die "Cannot open file: $!";
        
        while (my $line = <FILE>) {
            if ($line =~ /$ligand/)
            {
            $count++;
            $first=substr($line, 0,1);
            if($first=='H');
            {
            $sum++;
            }
            }
            print "Total No. of interactions are $count";
            print " No. of Hydrogen bonds are $sum";
        }
        close(FILE);
    }   
}

##Slurps a file into a list
sub slurp {
    my ($file) = @_;
    my (@data, @data_chomped);
    open IN, "<", $file or croak "can't open $file\n";
    @data = <IN>;
    for my $line (@data){
        chomp($line);
        push (@data_chomped, $line);
    }
    close IN;
    return (@data_chomped);
}
[download]

The messages you receive tell exactly what's wrong:

Global symbol "$count" requires explicit package name at test.pl line 
+14.
Global symbol "$first" requires explicit package name at test.pl line 
+15.
Global symbol "$first" requires explicit package name at test.pl line 
+16.
syntax error at test.pl line 16, near ");"
Global symbol "$sum" requires explicit package name at test.pl line 18
+.
Global symbol "$count" requires explicit package name at test.pl line 
+21.
Global symbol "$sum" requires explicit package name at test.pl line 22
+.
[download]

Define $count, $first and $sum, like the other variables in your script. For example, add the following line in the appropriate place:

my ($count, $first, $sum);

Next, No semi colon required here:

if ($first=='H');
{
[download]

Should be:

if ($first=='H')
{
[download]

I suggest spending some time working on the basics:

• perlintro
• http://learn.perl.org
• http://perldoc.perl.org
• Browse the Tutorials section of this site.

It worked. Superb. 
 Thank you so much. 
 
 Cheers 
 Miss Girl 
 

Can I ask you for a stupid type of help? Can you explain me the program as I am new to Perl programming. I just need to know how sub-function is working?

Thanks and Regards, 
 Rmgzsm9

The sub function basically receives the file as input, and then parses the data into an array, or list. The list is returned as output and is easier to go over.
This type of file parsing is called slurp

Also, if you want to get better at Perl, I highly recommend this book.
It really helped me out when I started learning Perl, and it will give you many valuable tools when you need to process biological data.
Good luck
Mr Guy