[BioPython] Help a clueless newbie with BLAST queries?

[Brad Chapman]

Hey all;
    Sorry to be jumping into this late -- had to travel to 
oh-so-exciting-and-beautiful West Virginia this weekend for a wedding, 
so I'm still catching up.

bp:
> > 1)The parser (b_parser) craps out with an "unexpected end of stream"
> 
> > 	save_handle = copy.deepcopy(b_results)
> > 	print 'writing from handle copy to output file\n'
> > 	save_file.write(save_handle.read())

Jeff: 
> You can't actually copy a handle like this.  Since you're already reading
> the contents of the handle, the blast parser has nothing left to read and
> complains.

Uck, sorry about this -- the bad example is definately mine. I just
fixed the example and Tutorial to use a strategy that actually works,
and got rid of all the deepcopy nonsense which I like so much, even
when it doesn't work :-).

So, you should be able to grab a new copy of the Tutorial from the
wiki pages, and the fixed example is in CVS. I also fixed another
problem area in the Tutorial that Iddo pointed out to me.

Let me know if you find any other sections in the Tutorial which are
confusing/just plain wrong; I'd definately like to fix all of my mistakes!

[remote BLAST scripts busted]
Jeff:
> Yep.  The format changed on us again.  I've updated the code to work with
> the new format.  I've checked it into CVS, and it should propogate to the
> anonymous server in a few hours.  Please try this and let me know if it
> works for you.

Thanks for the fix, Jeff! Seems to work snazzily for the example
script. 

No-more-driving-10-hours-through-the-mountains-for-me-ly yr's,
Brad