[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
http://bugzilla.open-bio.org/show_bug.cgi?id=2228
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
option.
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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