no element found at line 1, column 0, byte 0 at /usr/local/lib/perl5/site_perl/5.8.8/i686-linux/XML/Parser.pm line 187

#!/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");
}
    

<?xml version="1.0"?>
<!DOCTYPE eSearchResult PUBLIC "-//NLM//DTD eSearchResult, 11 May 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd">
<eSearchResult>
    <Count>1</Count>
    <RetMax>1</RetMax>
    <RetStart>0</RetStart>
    <IdList>
        <Id>29427659</Id>
    </IdList>
    <TranslationSet>
    </TranslationSet>
    <TranslationStack>
        <TermSet>
            <Term>140U_DROME[All Fields]</Term>
            <Field>All Fields</Field>
            <Count>1</Count>
            <Explode>Y</Explode>
        </TermSet>
        <OP>GROUP</OP>
    </TranslationStack>
</eSearchResult>

#!/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();
   }

}
   

 TwigHandlers => {
             
    "eSearchResult/IdList/Id" => \&id_Tag
             
}

#!/usr/bin/perl

use strict;
use warnings;
use XML::Twig;

 my $twig= XML::Twig->new(
                             TwigHandlers => {
                                "eSearchResult/IdList/Id" => \&id_Tag
                                             }
                         );

   $twig->parsefile("bla.xml") or die "cannot parse : $!";

sub id_Tag {
    my($t, $idTag)= @_;
    print $idTag->text(), "\n";
    # Release memory of processed tree up to here
    $t->purge();
}

###########################################
sub id_Tag {
###########################################
    my($t, $idTag)= @_;
    unless($idTag->text()) {
        print "ID-tag leer\n";
    }
    print $idTag->text(), "\n";
    
    # Release memory of processed tree up to here
    $t->purge();
}