[Genquire-dev] Loading TIGR xml into genquire

[Links M]

> Suddenly someone is back working on Genquire again!
>  Hurray! (It makes my CV look much better if the project
> is not dead.)

Lol. I am working on wavelet stuff for my thesis and I want
to use Genquire to let me view and integrate data. 

> Okay, TIGR xml - is that the SAX parser I wrote once ages
> ago?

No. The xml parsing is being done via Bio::SeqIO::tigr.
Which for reasons I do not understand seems to be a
line-by-line parse of the xml. Why you wouldn't just use
something like XML::Simple ...

> Or has someone thankfully updated it?

The latest person to be working with this was Simon Chan.
I've been talking to him already about things. 

> I had no idea what I was doing when I wrote that (come to

> think of it....), I just hacked at it until it worked
with
> the XML I was getting at the time.

That seems like ages ago doesn't it?

> Does it have something to do with the direction of the
> sequence?

I don't think so. There are soooooo many issues I'm
smashing my head into at the moment. 

> perl -d is your friend... but you know that.

I think we need a -hammer option. 
 
> You can send me code snippets if it will make you feel
> better.

At the moment I think I need to hit Simon up again to see
he's got any further ideas.

cheers,

Matt