#!/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::Simple;

#==============================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].xml");

    print FILE $raw;
    
    # create object
    my $xml = new XML::Simple or die "new failed";
 
     # read XML file
     my $data = $xml->XMLin("$record->[0].xml") or die "parse failed";
 
     # access XML data
    print "$data->{Id} \n";
    
    close FILE;
    unlink("$record->[0].xml");
}