[Biopython-dev] Removing obsolete bits of the Tutorial

Peter biopython at maubp.freeserve.co.uk
Fri Jun 27 15:42:16 UTC 2008

I'm still in documentation mode, and I've just removed bits of
documentation of a few deprecated or obsolete bits of code.

I've just got the the "BioRegistry – automatically finding sequence
sources" section of the tutorial/cookbook, and this either needs major
updating or removing.  First of all since Biopython 1.44, the line
"from Bio import db" had to be "from Bio.config.DBRegistry import db".
 And secondly, given this is all based on Martel parsers, the list of
supported formats is now a lot thinner.

Would anyone object to me removing this section of the
tutorial/cookbook?  We might be able to deprecate it too, but I'm not
sure what side effects that might have so its a bit risky this close
to a planned release.

Then there is the section on "Parser Design" which focuses on the
scanner/consumer model and lists lots of the events these parsers
(used to) generate.  I don't think any of this is useful, and suspect
that a lot of it is out of date.  Again, should we just remove this


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