[Biopython-dev] [Bug 1942] GenBank RecordParser fails on blank lines in features

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

http://bugzilla.open-bio.org/show_bug.cgi?id=1942


lpritc at scri.sari.ac.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
         OS/Version|All                         |Linux
           Platform|All                         |PC




------- Comment #6 from lpritc at scri.sari.ac.uk  2006-02-10 07:18 -------
Hi Peter,

I normally update biopython incrementally from CVS using `cvs update`, and the
last update I made was February 8th.  I also downloaded the source for
__init__.py v1.57 via ViewCVS from the BioPython site, and ran a diff against
the installed versions:

[lpritc at lplinuxdev downloads]$ diff __init__.py
/usr/lib/python2.4/site-packages/Bio/GenBank/__init__.py
[lpritc at lplinuxdev downloads]$ diff __init__.py
/usr/lib/python2.3/site-packages/Bio/GenBank/__init__.py

Neither run reported any differences.

The NCBI files are downloaded by ftp in BIN mode direct to the Linux box I work
on.  Checking the offending record with khexedit shows that the two linebreaks
are both CRs (0a), which you would expect to be handled equivalently on Windows
and Linux.  The NC_007633.gbk file I'm using has the same date as yours.

Running unix2dos, then attempting to parse, and dos2unix, and attempting to
parse, on a freshly-downloaded copy of NC_007633.gbk threw the same error in
each case on Linux:

>>> parser.parse(fhandle)
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "Bio/GenBank/__init__.py", line 212, in parse
    self._scanner.feed(handle, self._consumer)
  File "Bio/GenBank/__init__.py", line 1630, in feed
    assert line[0:FEATURE_QUALIFIER_INDENT]==FEATURE_QUALIFIER_SPACER, \
AssertionError: Expected qualifier description continuation, not:

I get the same error message using the same file on Windows, even after
conversion with unix2dos, and on Mac OS X with a fresh download of
NC_007633.gbk via ftp, and fresh install of biopython from CVS.

I must say I'm baffled as to why I'm getting a different result to you on this
file.  On the bright side, it's the only current bacterial genome .gbk file I'm
having a problem with.




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