[Biopython-dev] [Bug 2228] New: genbank parser should not print warnings to stdout

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Sun Mar 11 17:44:58 UTC 2007


           Summary: genbank parser should not print warnings to stdout
           Product: Biopython
           Version: 1.24
          Platform: PC
        OS/Version: FreeBSD
            Status: NEW
          Severity: critical
          Priority: P1
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: markd at cse.ucsc.edu

In general, it's not a good idea to print warnings from a library, as this is a
an undocumented and unexpected output from the library API.  However printing
warnings to stdout is a serious bug, meaning programs using the library can't
be used in a pipeline.

There are four warning prints to stdout in Bio/GenBank/__init__.py.  All of
these  should go to stderr, and probably be under the control of the debug

Also, the warning:
   "WARNING - Unquoted multiline '%s' entry for %s feature with location %s"
should be removed.  This is not a WARNING, it's a failure of this module to
correctly handle the poorly documented Genbank flat-file format

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