[Biopython-dev] test_ParserSupport.py

[Michiel de Hoon]

Bio.Emboss.Primer was also deprecated in 1.48 (replaced by Bio.Emboss.Primer3 and Bio.Emboss.PrimerSearch).

--Michiel.


--- On Tue, 9/23/08, Peter <biopython at maubp.freeserve.co.uk> wrote:

> From: Peter <biopython at maubp.freeserve.co.uk>
> Subject: [Biopython-dev] test_ParserSupport.py
> To: "BioPython-Dev Mailing List" <biopython-dev at lists.open-bio.org>
> Date: Tuesday, September 23, 2008, 12:04 PM
> The module Bio/ParserSupport.py provides general code for
> scanner/consumer parsers (some of which historically have
> been written
> using Martel).  It is used in several pure python parsers
> (e.g.
> Bio.SwissProt).  However, Tests/test_ParserSupport.py (its
> unit test)
> did use Martel explicitly for the EventGenerator class, and
> would fail
> if mxTextTools is not installed.  I have removed this part
> of the test
> in CVS.
> 
> Looking over the codebase with grep, EventGenerator is used
> in:
> * Bio.ECell (deprecated in 1.46)
> * Bio.Emboss.Primer [STILL CURRENT]
> * Bio.IntelliGenetics (deprecated in 1.48)
> * Bio.MetaTool (deprecated in 1.48)
> * Bio.NBRF (deprecated in 1.48)
> 
> It looks like Bio.Emboss.Primer is the only current bit of
> code using
> Bio.ParserSupport.EventGenerator, so it would be nice to
> still have
> this covered by the unit test.  Does anyone fancy
> re-writing the
> EventGenerator part of unit test?  I think this could be
> done by
> creating a simple python Scanner object...
> 
> Peter
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