=head1 MySAXHandler

MySAXHandler is a little package to describe what to do with the event
+s generated by the SAX parser.
All events are treated by methods described here. MySAXHandler is inst
+anciated in the parser declaration.

Variable %entryArgs keeps data until end_element = 'entry' event and t
+hen it writes data. It's keys are :

=over 3
  =item 'Accession' which is a hash structure also as there can be mor
+e than one accession number for each entry. Accession number is hold 
+in the key, and value is empty.
  =item 'Organism' which stores the organism name
  =item
  =item
  =item 

=back

Other variables used in this package

=over 3
  
  =item $currentElement : Stores the Name of the current element
  =item $currentAttributes : Store a hash reference towards the curren
+t element's attributes
  =item $entryCounter : counts <entry> tags seen
  =item $entryDone : counts </entry> tags seen
  =item $dbReferenceOn : Set to 1 if we are in a <dbReference> ... </d
+bReference> block
  =item $comment : as above for <comment> ... </comment>
  
=back

=head1 Methods

=cut

package MySAXHandler;
use base qw(XML::SAX::Base);

$|=1;

my (%entryArgs);
my (
    $currentElement, $currentAttributes, $entryCounter,
    $entryDone,      $accessionNumber,   $currentAttrs
);
my ( $dbReferenceOn, $commentOn, $organismOn ) = ( 0, 0, 0 );

=head2 start_document

For us this method does nothing for now.

=cut

sub start_document {
    my ( $self, $doc ) = @_;

    #What to do with the document start
    print "Here we go ..............\n\n";
}

=head2 start_element

Event 'start_element' calls this function.
Depending on the tag Name, it does various things.
Tag name is stored into $currentElement. It's attributes into $current
+Attributes.

=cut

sub start_element {
    my ( $self, $el ) = @_;

    #clear %entryArgs when start_element = <entry>
    if ( $el->{Name} eq 'entry' ) {
        undef(%entryArgs);
        $entryCounter++;
    }

    #Set the current element name and attributes
    $currentElement = $el->{Name};

    #print $el->{Name}."\n";

    $currentAttributes = $el->{Attributes};

#    foreach my $key (keys %{$currentAttributes}) {
#            print "===============$key => ".%{$currentAttributes}->{$
+key}->{Value}."================\n";
#        }

    #Set some flag to 1 for interesting blocks
    $dbReferenceOn = 1                  if ( $el->{Name} eq 'dbReferen
+ce' );
    $commentOn     = 1                  if ( $el->{Name} eq 'comment' 
+);
    $organismOn    = 1                  if ( $el->{Name} eq 'organism'
+ );
    $organismAttrs = $currentAttributes if ( $el->{Name} eq 'name' );
}

=head2 end_element

Store data into the dB, and prints out if tag name = entry.

Set flags back to 0.

=cut

sub end_element {
    my ( $self, $el ) = @_;

    #What to do now ... print out or store in dB
    if ( $el->{Name} eq 'entry' ) {
        print "Accession number(s) :\n";
        foreach my $key ( sort keys %{ $entryArgs{'Accession'} } ) {
            print "\t=>$key\n";
        }

        print "\n\tOrganism Name = " . $entryArgs{'Organism'} . "\n";
    }

    #foreach my $key (sort keys %entryArgs) {

    #Store Accession Number
    $entryArgs{'Accession'}{$accessionNumber}++
      if ( $el->{Name} eq 'accession' );
    undef($accessionNumber) if ( $el->{Name} eq 'accession' );

    #Set the flags back
    $dbReferenceOn = 0 if ( $el->{Name} eq 'dbReference' );
    $commentOn     = 0 if ( $el->{Name} eq 'comment' );
    $organismOn    = 0 if ( $el->{Name} eq 'organism' );
}

=head2 characters

Store data into the entryArgs hash.

=cut

sub characters {
    my ( $self, $char ) = @_;
    my $text = $char->{Data};

    #Store accesion number
    if ( $currentElement eq 'accession' ) {
        $accessionNumber .= $text;

        $accessionNumber =~ s/[\s\r\n]//g;
    }

    #Store organism name
    if ( $organismOn == 1 and $currentElement eq 'name' ) {
        if ( $organismAttrs->{'{}type'}->{Value} eq 'scientific' ) {
            $entryArgs{'Organism'} .= $text;
        }
    }

}

sub end_document {
    my ( $self, $doc ) = @_;

    print "\n\n ...................... et voilą ;-)\n";
}
[download]

#!/usr/bin/perl -w

# POD documentation - main docs before the code

=head1 NAME

parseUNIPROT4MySQL

=head1 DESCRIPTION

This script parse the XML file containing uniprot knowledgebase, fetch
+ informations ad insert them
into a MySQL db.

=head1 CONTACT

TEXTORIS Julien , <julien.textoris@gmail.com>

=head1 USAGE

./parseUNIPROT4MySQL.pl <XML_filename> <function>

function :
    - 'coordinate'
    - 

=cut

use strict;
use warnings;
use DBI;
use XML::SAX;
use lib './';
use MySAXHandler;

$|=1;

=head1 Variables Declaration

=over 3
 =item $filename : XML file to parse
 =item $function : implemented function to use
 =item $dbd : MySQL connection
 =item $dbname : DB Name
 =item $host : computer which host the database
 =item $user / $pass : user and password to connect DB
 =item $insert_ensembl = Insert EnsEMBL_ID into ensEMBL_ID table if it
+ doesn't exists
 =item $insert_uniprot = Insert Uniprot_ID into Uniprot_ID table if it
+ doesn't exists
 =item $insert_relEnsemblUniprot = insert values into the relational t
+able (n:m relation)
 =item $parser = new XML parser object
 =item $doc = XML object loaded from $filename, option strip whitespac
+e make parsing 30% faster
 =item $rootNode = XML root tag
 =item $AccNumber = store Uniprot Accession number of entry being proc
+essed
 =item $type = type argument of <comment> tag
 =item $value = value of <text> tag of a given comment tag

=back
 
=cut

my $filename = $ARGV[0];
my $function = $ARGV[1];
my $dbname   = "AnnotationDB";
my $host     = "localhost";
my $user     = "jtextori";
my $pass     = "marcel";

#my $dbd = DBI->connect( "DBI:mysql:$dbname;host=$host",
#    $user, $pass, { RaiseError => 1 } )
#  or die
#  "can't connect : \nerror1 ==> $DBI::errstr\nerror1 ==> $@\nerror1 =
+=> $!\n\n";
#
#my $insert_ensembl = $dbd->prepare('INSERT INTO ensEMBL_ID (`ensEMBL_
+ID`) VALUES (?)');
#my $insert_uniprot = $dbd->prepare('INSERT INTO Uniprot_ID (`Uniprot_
+ID`) VALUES (?)');
#my $insert_relEnsemblUniprot = $dbd->prepare('INSERT INTO ensEMBL_ID_
+has_Uniprot_ID (`ensEMBL_ID_ensEMBL_ID`,`Uniprot_ID_Uniprot_ID`) VALU
+ES(?,?)');

my $parser = XML::SAX::ParserFactory->parser(Handler => MySAXHandler->
+new);
$parser->parse_uri($filename);

exit(0)
[download]