[Biopython-dev] [Bug 2481] bitscore not parsed.

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2481


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #6 from biopython-bugzilla at maubp.freeserve.co.uk  2008-04-07 09:46 EST -------
I've checked this in to CVS (taking note of Michiel's comments), and confirmed
the NCBI XML unit test passes.

Sebastian - could you submit your suggested changes as patches next time
please?  It would have made life a little easier, trying to work out what
exactly you wanted to change (which in the end, was fairly small).

> 1) In NCBIXML.py:
> method = self._secure_name('_end_' + name.replace("-","_"))
> I don't see why name.replace("-","_") is needed. Isn't that the purpose of
> self._secure_name in the first place?

I agree.

> 2) In Record.py:
> Please add "bits" with a description to the docstring (lines 58-65).

I've done this in CVS.

> 3) About your change:
> > Lines 409-410 uncommented
> I wonder why these lines were commented out in the first
> place. It was done in revision 1.8 of NCBIXML.py, but I
> didn't see any explanation as to why those lines were
> commented out. Peter, do you know?

I made that old check-in, but it was some time ago and I don't recall the
details.  The self._descr.bits variable was never setup, causing an exception,
and I guess at the time uncommenting this bit seemed like a good solution.

With the Record.py fixed, the parser lines can now be uncommented.  Perhaps the
original code used to work on early NCBI XML files?

Marking as fixed.


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