[Biopython-dev] [Bug 1654] New: SyntaxError in NCBIWWW.BlastParser

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

http://bugzilla.open-bio.org/show_bug.cgi?id=1654

           Summary: SyntaxError in NCBIWWW.BlastParser
           Product: Biopython
           Version: Not Applicable
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: critical
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: idoerg at burnham.org


>>> file = open("results")
>>> from Bio.Blast import NCBIWWW
>>> parser = NCBIWWW.BlastParser()
>>> parser.parse(file)
Traceback (most recent call last):
 File "<stdin>", line 1, in ?
 File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIWWW.py", line 47, in parse
   self._scanner.feed(handle, self._consumer)
 File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIWWW.py", line 99, in feed
   self._scan_rounds(uhandle, consumer)
 File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIWWW.py", line 242, in
_scan_rounds
   self._scan_alignments(uhandle, consumer)
 File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIWWW.py", line 325, in
_scan_alignments
   self._scan_pairwise_alignments(uhandle, consumer)
 File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIWWW.py", line 348, in
_scan_pairwise_alignments
   self._scan_one_pairwise_alignment(uhandle, consumer)
 File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIWWW.py", line 379, in
_scan_one_pairwise_alignment
   self._scan_alignment_header(uhandle, consumer)
 File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIWWW.py", line 417, in
_scan_alignment_header
   raise SyntaxError, "I missed the Length in an alignment header"
SyntaxError: I missed the Length in an alignment header



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