Hi!

So, I admit I am a little new to perl, but I think I can communicate what I need to be done just fine, so be a little patient with me. And I am sorry it's a little long.

What I am trying to do is successfully parse an XML file. I figured that I can do it with XML::Simple module and together a friend and I have successfully put together something that does just that, but it's a little messy. So here's where we'd like to go next.

1) So, the XML file is 2 gigs. And to grab information from it, it needs to through line by line. I know XML::Simple puts everything into a hash, but it's behaving very poorly. (I'll show why below). What I want to do, is to be able to jump to a specific line in a file. So, for example, I get input A, I need somehow to know that more information about Input A is located at some line in the file, which I will call B. So, what I want to know is the byte location of line B. I know how to find the line that I want using XML::Parser and handlers, but I don't know how to get this byte location and later how to jump to it.

B) If that's not possible, then here's what I mean by the code being messy. This in a excerpt.

 
# read XML file
    $data = $xml->XMLin($contents, keyattr => {property => 'type'});


    
    # finding protein names
    @names = ();
    
    $names_ref = $data->{entry}->{protein}->{name};
    
    if (ref($names_ref) eq 'ARRAY')        ## more than one name
    {
        @nameArray = @$names_ref;        ## so derefrence to array and
+ step through
        
        foreach $nameA_ref (@nameArray)
        {
            if (ref($nameA_ref) eq 'HASH')    ## it shouldn't be a has
+h, but sometimes it is
            {
                %nameTable = %$nameA_ref;
                push (@names, $nameTable{"content"});
            }
            else    ## it is a friendly scalar
            {
                push (@names, $nameA_ref);
            }
        }
    }
    else        ## only one name, so $names_ref is probably a scalar
    {
        if (ref($names_ref) eq 'HASH')    ## it shouldn't be a hash, b
+ut sometimes it is
        {
            %namesTable = %$names_ref;
            push (@names, $namesTable{"content"});
        }
        else    ## it is a friendly scalar
        {
            push (@names, $names_ref);
        }
}
[download]

This is how the data is being processed in teh file. I am not sure why a 'HASH' or sclar suddenly comes up. I've been trying to figure out it ForceArray does anything, and kinda how to use it. So far it's only given errors, even though I think I've been using it right.

Anyway the above method does seem to work, but it's just not very nice. I can't change the XML in anyway, so maybe it's not suppose to be very nice to grab info out and maybe our method is right. I appreciate any help. If curious, a sample of the XML format is here, http://beta.uniprot.org/uniprot/P15455.xml

Thanks!