Hi perlmonks.... I want to ask concerning a flat file database whose records are separated by "//\n" ( double slash and new line). I have a very huge database (input.db) looks partly like: 
COMMERCIAL SUPPLIERS
SEQUENCE             /toxin_start="19-94"
                     /translation="MKFFLMCLIIFPIMGVLGKKNGYPL          
+           CWGACYCFGLEDDKPIGPMKDITKKYCDVQIIPS"
AA ALIGNMENT
full-length{%scorpProtein}, sodium-family{%scorpNA}, putative-group1{%
+Nag01}, putative-group1c{%Nag01c}
ORIGIN      
   1 acaaaataaa gtgaacttct gaaatcagca cgataaaaag aaacgaaaat gaaatttttc
//
COMMERCIAL SUPPLIERS
SEQUENCE             /toxin_start="19-94"
                     /fragment_start="?"
                     CWGACYCFGLEDDKPIGPMKDITKKYCDVQIIPS"
AA ALIGNMENT
full-length{%scorpProtein}, sodium-family{%scorpNA}, putative-group1{%
+Nag01}, putative-group1c{%Nag01c}
ORIGIN      
        1 aaaataaagt gaacttctga aatcagcacg ataaaaagaa acgaaaatga aattt
+ttctt
       61 aatgtgtctt atcatcttcc caattatggg agtgcttggc aaaaagaacg gatat
+cctct
//

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I'm going to read the input, make some changes and then write it back to the output files. I am a little bit confused with the input separator since at first I have set it to //\n and then for each records I want to examine it line by line.

I have tried to put a counter in my code but there the program never stop running. 

I compile the prog using: perl prog.pl input.db result

#!/usr/bin/perl

my $input = $ARGV[0];
my $output = ">" . $ARGV[1];
my $counter=1;

open(INPUT, $input) or die "Can't open $input.";
open(OUTPUT, $output) or die "Can't open $output.";

$/="\/\/\n";

# Use shorthand for reading file.
while (<>) {
    print OUTPUT $_;
    print $counter;
    $counter++;
}
print "Success\n";
close (INPUT);
close (OUTPUT);

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I have tried to do 
>
while(<INPUT>)

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instead of just while(<>) but it only print the counter once. Is there something wrong with the code? And if I want to read/modify each line in the record where should I set the $\ back to \n? Thank you in advanced.

Sincerely

In reply to about separator by agustina_s

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