[BioPython] Different parse error in ace.py

[Frank Kauff]

Leighton,

On Mon, 2004-04-19 at 09:05, Frank Kauff wrote:
> Hi Leighton,
> 
> On Mon, 2004-04-19 at 08:34, Leighton Pritchard wrote:
> > -----BEGIN PGP SIGNED MESSAGE-----
> > Hash: SHA1
> > 
> > Hi all,
> > 
> > The Ace.py parser assumes that the DS tag will always be present in
> > Phrap output.  Unfortunately, it isn't always present in my output, and
> > so the parser gave me this traceback:
> > 
> 
> Thanks for pointing this out. Ace parsing is learning by doing -
> unfortunately there's no proper description of which tags appear when
> and where... I indeed assumed that there's always a DS. I'll update the
> code, so far your workaround seems to the right thing to do.
> 

Just had a look at the parser and it seems that it is unfortunately a
bigger problem. The way the read data (rd, qa, ds) is currently stored
assumes that there's the same number of rd, qa and ds records for each
read. Storing an empty DS would be a possibility, but is pretty
unelegant. Anyway, I was feeling more and more uncomfortable with the
way ace.py is storing data for record - now I have a reason for
restructuring it :-)

F.

-- 
Frank Kauff
Dept. of Biology
Duke University
Box 90338
Durham, NC 27708
USA

Phone 919-660-7382
Fax 919-660-7293