[Biopython-dev] [Bug 2289] Can't parse GenBank files with "ss-cRNA" in the LOCUS line

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2289


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

           What    |Removed                     |Added
----------------------------------------------------------------------------
           Severity|blocker                     |normal
             Status|ASSIGNED                    |RESOLVED
         OS/Version|Windows XP                  |All
           Platform|PC                          |All
         Resolution|                            |FIXED
            Summary|LOCUS ss-cRNA => ERROR      |Can't parse GenBank files
                   |                            |with "ss-cRNA" in the LOCUS
                   |                            |line
            Version|1.24                        |Not Applicable




------- Comment #3 from biopython-bugzilla at maubp.freeserve.co.uk  2007-05-09 10:48 EST -------
See also Bug 2231. With hindsight checking against a known list of sequences
types was too harsh.  It now just looks for the text "DNA" or "RNA" within this
field of the LOCUS line in GenBank files.

I've checked in a fix to CVS, and checked I can parse GenBank file NC_005236

The simplest way to update your machine Daniel is to download and replace the
file D:\Python25\lib\site-packages\Bio\GenBank\Scanner.py with revision 1.11
from here:

http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/GenBank/Scanner.py?cvsroot=biopython

There will be a slight time delay before the CVS web site updates itself - you
can of course get the file sfrom CVS directly if you would rather.

Please let us know (on this bug) if that doesn't solve this problem.


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