What you actually are trying to do is a kind of streaming. I mean FileAPI is not suited for the task. Instead, I could suggest two options :
The first, using XHR facility, ie ajax, by splitting your data into several chunks which will sequencially be sent to the server, each chunk in its own request along with an id ( for identifying the stream ) and a position index ( for identifying the chunk position ). I won't recommend that, since it adds work to break up and reassemble data, and since there's a better solution.
The second way of achieving this is to use Websocket API. It allows you to send data sequentially to the server as it is generated. Following a usual stream API. I think you definitely need this.
This page may be a good place to start at : http://binaryjs.com/
That's all folks !
EDIT considering your comment :
I'm not sure to perfectly get your point though but, what about HTML5's FileSystem API ?
There are a couple examples here : http://www.html5rocks.com/en/tutorials/file/filesystem/ among which this sample that allows you to append data to an existant file. You can also create a new file, etc. :
function onInitFs(fs) {
fs.root.getFile('log.txt', {create: false}, function(fileEntry) {
// Create a FileWriter object for our FileEntry (log.txt).
fileEntry.createWriter(function(fileWriter) {
fileWriter.seek(fileWriter.length); // Start write position at EOF.
// Create a new Blob and write it to log.txt.
var blob = new Blob(['Hello World'], {type: 'text/plain'});
fileWriter.write(blob);
}, errorHandler);
}, errorHandler);
}
EDIT 2 :
What you're trying to do is not possible using javascript as said on SO here. Tha author nonetheless suggest to use Java Applet to achieve needed behaviour.
To put it in a nutshell, HTML5 Filesystem API only provides a sandboxed filesystem, ie located in some hidden directory of the browser. So if you want to access the true filesystem, using java would be just fine considering your use case. I guess there is an interface between java and javascript here.
But if you want to make your data only available from the browser ( constrained by same origin policy ), use FileSystem API.