[Biopython-dev] [Bug 1746] New: Again with the "Unexpected end of stream" when parsing Blast results

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

http://bugzilla.open-bio.org/show_bug.cgi?id=1746

           Summary: Again with the "Unexpected end of stream" when parsing
                    Blast results
           Product: Biopython
           Version: Not Applicable
          Platform: Macintosh
        OS/Version: MacOS X
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: plorch at email.unc.edu


This was Bug#1627. I just upgraded to 1.3.  I rediscovered this bug while running www_blast.py in 
Bio/Doc/examples.

Error code:
plorch% python www_blast.py
Doing the BLAST and retrieving the results...
Parsing the results and extracting info...
Traceback (most recent call last):
  File "www_blast.py", line 37, in ?
    b_record = b_parser.parse(string_result_handle)
  File "/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site-packages/Bio/
Blast/NCBIWWW.py", line 47, in parse
    self._scanner.feed(handle, self._consumer)
  File "/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site-packages/Bio/
Blast/NCBIWWW.py", line 96, in feed
    has_re=re.compile(r'<b>.?BLAST'))
  File "/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site-packages/Bio/
ParserSupport.py", line 335, in read_and_call_until
    line = safe_readline(uhandle)
  File "/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site-packages/Bio/
ParserSupport.py", line 411, in safe_readline
    raise SyntaxError, "Unexpected end of stream."
SyntaxError: Unexpected end of stream.



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