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

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

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


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
           Severity|critical                    |major
             Status|NEW                         |ASSIGNED




------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2007-03-11 14:31 EST -------
I don't think you are using BioPython 1.24, but probably 1.42 (I know, the
buzilla choices need updating).

Since the release of BioPython 1.42, this area of code has been revised
significantly (to also deal with EMBL files) and of those print statments have
either vanished or are debug only.  Have a look at new file
Bio/GenBank/Scanner.py

There is currently just one "evil print statement", triggered when faced with a
"minimal LOCUS line".  I will make this print to standard error instead...
I would very much like to have some examples of this as test cases BTW.

> Also, the warning:
> "WARNING - Unquoted multiline '%s' entry for %s feature with location %s"
> should be removed.

It has already been removed.

> This is not a WARNING, it's a failure of this module
> to correctly handle the poorly documented Genbank flat-file format

Unqoted multiline feature entries do exist "in the wild" but are in breach of
my reading of the NCBI documentation.  The parser handles them fine (but
grumbled).


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