[BioPython] new parser questions

[clee@spiralis.merseine.nu]

Brad Chapman writes:
 > Hey Chris;
 > 
 > > I have more parser questions too.  I'm a bit behind current progress,
 > > but last time I looked at BioPython a few months ago, the parser I
 > > looked at seemed to be highly line-oriented.  
 > 
 > True enough. But then again, most of the files that we need to parse are
 > also line oriented....

Definitely makes sense to use the line oriented parser w/
line-oriented files.


 > ...It depends how you want to think about it. This approach allows us to
 > say: "Look, the format has changed. We need to check the parser to make
 > sure it is still doing the right thing." With the current framework,
 > changes are easy to isolate and check; the last thing we want is to have
 > the parser happily parsing a file it doesn't understand and giving
 > incorrect output...

I guess I hadn't thought of it that way---I still tend to believe that
parsing the html aspect of things first might be helpful.  Extracting
data from it would still require painful special case work.  Maybe
I'll look at it <grimace/>.


 > BLAST parsing is also done under the old Producer/Consumer framework.
 > Currently, we develop parsers using Martel...

Thanks Brad for the response.  I'll look at Martel.

-chris