[Biopython-dev] [Bug 3176] New: Bio SeqIO 'genbank' parse failure

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

http://bugzilla.open-bio.org/show_bug.cgi?id=3176

           Summary: Bio SeqIO 'genbank' parse failure
           Product: Biopython
           Version: 1.56
          Platform: Macintosh
        OS/Version: Mac OS
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: sschmidt at tuebingen.mpg.de


Hi,

the parser stumbles over a Genbank file that contains a feature without values:

___START GenBank File____
LOCUS       someVector______        6127 bp    DNA     circular      1-OCT-2009
SOURCE      
  ORGANISM  
COMMENT     none
FEATURES             Location/Qualifiers
     misc_structure  1564..1566
                     /ApEinfo_label=ErrorInBioPythonBecauseNoValue
                     /ApEinfo_fwdcolor=
                     /ApEinfo_revcolor=
                     /vntifkey="88"
                     /label=Stop\codon
BASE COUNT       15 a      16 c      16 g      13 t 
ORIGIN
        1 gagttccgcg ttacataact tacggtaaat ggcccgcctg gctgaccgcc caacgacccc 
 //
__END GenBank file___


The relevant error message:
  File "/sw/lib/python2.7/site-packages/Bio/SeqIO/__init__.py", line 525, in
parse
    for r in i:
  File "/sw/lib/python2.7/site-packages/Bio/GenBank/Scanner.py", line 437, in
parse_records
    record = self.parse(handle, do_features)
  File "/sw/lib/python2.7/site-packages/Bio/GenBank/Scanner.py", line 420, in
parse
    if self.feed(handle, consumer, do_features):
  File "/sw/lib/python2.7/site-packages/Bio/GenBank/Scanner.py", line 392, in
feed
    self._feed_feature_table(consumer, self.parse_features(skip=False))
  File "/sw/lib/python2.7/site-packages/Bio/GenBank/Scanner.py", line 188, in
parse_features
    features.append(self.parse_feature(feature_key, feature_lines))
  File "/sw/lib/python2.7/site-packages/Bio/GenBank/Scanner.py", line 268, in
parse_feature
    elif value[0]=='"':
IndexError: string index out of range


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