#!/usr/local/bin/perl -w

#use strict;
#use warnings;
use DBI;
use Net::MySQL;
use HTTP::Request::Common;
use LWP::UserAgent;
use CGI qw(header -no_debug);
use XML::Twig;

#==============================database connection================================================


#=============================end database connection==================================================


$mysql->query(qq{SELECT accession_code FROM protein});

my $record_set = $mysql->create_record_iterator;

while (my $record = $record_set->each) {
   print "Accession ID: $record->[0] \n";
   
   #For retrieving data from a url post in perl, we will use the LWP module "get" function

   use LWP::Simple; #supports the "get" function

   $baseurl="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/";
   $eutil="esearch.fcgi?";
   $parameters="db=protein&term=$record->[0]&retmode=xml";        
   $url=$baseurl.$eutil.$parameters;

   $raw=get($url);
   
   open(FILE, ">$record->[0]");
    print FILE $raw;
    close FILE;
    
    $xml_file = $record->[0];
    
    my $twig= XML::Twig->new(
               
 TwigHandlers => {
               
     "/eSearchResult/IdList/Id" => \&id_Tag
               
 }
    );


    #actually parse the file
    $twig->parsefile($xml_file) or die "cannot parse [$xml_file]: $!";

    

    ###########################################
    sub id_Tag {
    ###########################################
      my($t, $idTag)= @_;

        print $idTag->text(), "\n";
      
      # Release memory of processed tree up to here
   $t->purge();
   }

}