[Biopython-dev] [Bug 2754] Bio.PDB: Parse warnings should print to stderr, not stdout

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Thu Feb 12 19:38:33 UTC 2009


------- Comment #8 from bsouthey at gmail.com  2009-02-12 14:38 EST -------
(In reply to comment #7)
> (In reply to comment #6)
> Also, as Bruce and Peter implied may happen, this patch clobbers test_PDB.py.
> Some options:
> 1. Redirect stderr to stdout, and modify Tests/output/test_PDB to match again.
> 2. Change test_PDB.py to check the exceptions separately, maybe converting it
> to a unittest-style test in the process. Maybe also splitting a_structure.pdb
> into multiple files, with one bug each.

You know more about this than I do. But I think that test_PDB.py must get
rewritten partly because of the text it prints and lack of coverage (like
retrieving PDB file online). But really it should be checking these corner
cases are handled correctly. So if it is an error in PDB file then the test
should check that the error reported is the correct message for that error. 

For example, running the test from the command line the first message is:
PDBConstructionException: Atom N defined twice in residue <Residue ARG het= 
resseq=2 icode= > at line 19.
Exception ignored. 

Is that correct or desired output? 
The actual error is in my mind irrelevant although I do wonder why a special
exception is used.

(In reply to comment #6)
There are a few cases of this so I think a separate bug should be filed. But
cleaning these up would be appreciated, at least by me.

Just my couple of cents,

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