Hi Perlmonks ..... I have a problem concerning a very big database consists of a lot of records which is separated by //and\n. The input database looks partly like:

DATE  13-JUN-2000
  AUTHORS   Oren,D.A., Froy,O., Amit,E., Kleinberger Doron,N., Gurevit
+z,M. and Shaanan,B.
ORIGIN      
   1 acaaaataaa gtgaacttct gaaatcagca cgataaaaag aaacgaaaat 
  51 ttaatgtgtc ttatcatctt cccaattatg ggagtgcttg gcaaaaagaa 
//
DATE  13-JUN-2000
  AUTHORS    Froy O, Zilberberg N, Gordon D, Turkov M, Gilles N, Stank
+iewicz M, Pelhate M, Loret E, Oren DA, Shaanan B, Gurevitz M.
GenBank:AJ012313{%3858952&dopt=GenBank}, EMBL:AJ012313{%AJ012313}, DDB
+J:AJ012313{%AJ012313}, SwissProt:P56637{%P56637}
ORIGIN
   1 aaaataaagt gaacttctga aatcagcacg ataaaaagaa 
//
[download]

I want to do some changes to the input and then print it to the output files. I have some problem with the input separator. At first I set it to "//\n" but then inside the for loop I want to examine for every line in the prog. So do I have to set it back to \n? And I have some trouble with the while loop. My code looks like:

compile : perl prog.pl input.db result 

#!/usr/bin/perl
my $input = $ARGV[0];
my $output = ">" . $ARGV[1];
my $counter=1;
my $no='D000001';

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

$/="//\n";
while (<INPUT>) {
    print "DBACC\t $no\n";
    if ($_=~/^DATE\s*(.*-.*-.*)\s*\n/){
        print "DATE\t $1\n";}
    elsif ($_=/^GenBank:(.*),\sEMBL:(.*),\sDDBJ:(.*)},\sSwissProt:(.*)
+\n/){
    print "ACCESSION:GenBank\t ($1)\n";
    print "ACCESSION:EMBL\t ($2)\n";
    print "ACCESSION:DDBJ\t ($3)\n";
    print "ACCESSION:SwissProt\t ($4)\n";
    }
    print "Entry $counter\n";
    $counter++;
    $no++;
   }
close (INPUT);
close (OUTPUT);
[download]

But the program only loop once and only print the DBACC not even the date. When I set the input separator back into \n in the loop it also didn't give many changes. Where do I have to put the input separator so that for each record I can modify the line and print it back to the output?

Thanks in advanced. Sincerely

Ti2xn