[Biopython-dev] [Bug 1608] New: NCBIStandalone.py dies parsing long blastpgp -m6 output

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

http://bugzilla.bioperl.org/show_bug.cgi?id=1608

           Summary: NCBIStandalone.py dies parsing long blastpgp -m6 output
           Product: Biopython
           Version: 1.24
          Platform: All
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: j.a.casbon at qmul.ac.uk


When using: 
    blastout = os.popen("zcat %s" % file) 
    b_parser = NCBIStandalone.PSIBlastParser() 
    b_iterator = NCBIStandalone.Iterator(blastout, b_parser) 
    for b_record in b_iterator: 
 
to parse blast output in multiple alignment format (-m6), the parser dies on 
some files, and not others.  It seems not to like longer files - but this is 
just my feeling. 
 
This is biopython 2.4 on debian linux unstable. 
 
I have  blast output that produces this bug available at: 
http://compbio.mds.qmw.ac.uk/~james/78700.blo.gz 
 
Here is the stack trace: 
  File "/home/james/exp/iss/shared_sequences", line 63, in get_seqs 
    for b_record in b_iterator: 
  File 
"/home/james/biopython-1.24/build/lib.linux-i686-2.3/Bio/Blast/NCBIStandalone.py", 
line 1332, in next 
    return self._parser.parse(File.StringHandle(data)) 
  File 
"/home/james/biopython-1.24/build/lib.linux-i686-2.3/Bio/Blast/NCBIStandalone.py", 
line 571, in parse 
    self._scanner.feed(handle, self._consumer) 
  File 
"/home/james/biopython-1.24/build/lib.linux-i686-2.3/Bio/Blast/NCBIStandalone.py", 
line 97, in feed 
    self._scan_rounds(uhandle, consumer) 
  File 
"/home/james/biopython-1.24/build/lib.linux-i686-2.3/Bio/Blast/NCBIStandalone.py", 
line 152, in _scan_rounds 
    self._scan_descriptions(uhandle, consumer) 
  File 
"/home/james/biopython-1.24/build/lib.linux-i686-2.3/Bio/Blast/NCBIStandalone.py", 
line 272, in _scan_descriptions 
    read_and_call_until(uhandle, consumer.description, blank=1) 
  File 
"/home/james/biopython-1.24/build/lib.linux-i686-2.3/Bio/ParserSupport.py", 
line 340, in read_and_call_until 
    method(line) 
  File 
"/home/james/biopython-1.24/build/lib.linux-i686-2.3/Bio/Blast/NCBIStandalone.py", 
line 637, in description 
    dh = self._parse(line) 
  File 
"/home/james/biopython-1.24/build/lib.linux-i686-2.3/Bio/Blast/NCBIStandalone.py", 
line 694, in _parse 
    dh.score = _safe_int(dh.score) 
  File 
"/home/james/biopython-1.24/build/lib.linux-i686-2.3/Bio/Blast/NCBIStandalone.py", 
line 1602, in _safe_int 
    return long(float(str)) 
ValueError: invalid literal for float(): 
RPVV----RDD-----R-------P----D----L-I-Y--R-----------T---MEG



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