[Biopython-dev] [Bug 1942] GenBank RecordParser fails on particular qualifier structure

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

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


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

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |DUPLICATE




------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk  2006-02-03 11:30 -------
Using the CVS copy of Bio/GenBank/__init__.py your example works for me. 
Please reopen the bug or follow up on the mailing list if that doesn't solve
the problem for you.

My copy of the NC_002758 GenBank file has the same "bad" note entry, it starts:

LOCUS       NC_002758            2878529 bp    DNA     circular BCT 19-JAN-2005

Sample output:

Python 2.3.3 (#51, Dec 18 2003, 20:22:39) [MSC v.1200 32 bit (Intel)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> from Bio.GenBank import RecordParser
>>> parser = RecordParser()
>>> record = parser.parse(file('NC_002758.gbk'))
>>> print record.features[1635]
     CDS             878043..878612
                     /locus_tag="SAV0800"
                     /note=" similar to bacteriophage terminase small subunit"
                     /codon_start=1
                     /transl_table=11
                     /product="similar to bacteriophage terminase small
                     subunit"
                     /protein_id="NP_371324.1"
                     /db_xref="GI:15923790"
                     /db_xref="GeneID:1120775"
                     /translation="MSELTAKQARFVNEYIRTLNVTQSAIKAGYSANSAHVTGCRLLK
                     KPHIKQYIQEQKDKIIDENVLTAKELLHVLTNAAVGDETETKEVVVKRGEYKENPQSG
                     KVQLVYNEHVELIEVPIKPSDRLKARDMLGKYHKLFTDKHDINGNVPIFINIGEWDGD
                     DEELDKTVKDVSNANPNHTVIVDDIPLED"

Notice that the original "bad" formating has not been preserved - which is
arguably a bug...

*** This bug has been marked as a duplicate of 1903 ***




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