[Biopython-dev] [Bug 2754] New: 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

           Summary: Bio.PDB: Parse warnings should print to stderr, not
                    stdout
           Product: Biopython
           Version: 1.49
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: eric.talevich at gmail.com


In Bio.PDB.PDBParser, and perhaps its neighbors, warnings raised while parsing
in permissive mode are printed to standard output. In general, messages like
this should be printed to standard error to avoid sending garbage to the next
program in a pipeline.

Recommendation: In PDBParser._handle_PDB_exception, change the print statements
to include ">>sys.stderr". Also track down other print statements in the PDB
module and send any other warnings to sys.stderr as well. (Grepping
Bio/PDB/*.py should work.)


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