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

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2754





------- Comment #10 from eric.talevich at gmail.com  2009-03-20 14:52 EST -------
Here's the github branch where I'm working on this bug:

http://github.com/etal/biopython/tree/master

I've applied the two patches attached here and converted the test script from
print-and-compare to unittest. The tests pass now, but I haven't added checks
for specific parsing errors, just the general PDBConstructionError raised when
parsing the example file with PERMISSIVE=0.

The warnings are hidden during tests, as expected, but in this branch the
PDBParser warnings are noticeably more annoying during normal use. Fixing this
will require more tweaking in Bio/PDB/PDBParser.py -- I'll do that in the same
branch, since I don't think you'd want to merge one fix without the other. Same
goes for the __debug__ protection in StructureBuilder.py.


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