[Biopython-dev] [Bug 2527] New: Bug in NCBIXML.py in _end_BlastOutput_version()

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Sun Jun 22 04:51:58 UTC 2008


           Summary: Bug in NCBIXML.py in _end_BlastOutput_version()
           Product: Biopython
           Version: 1.45
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: cdputnam at ucsd.edu

biopython version is from Fedora distribution:

For a recently run NCBIWWW Blast (following the tutorial at
http://biopython.org/DIST/docs/tutorial/Tutorial.html), I
ran into a problem in parsing by _end_BlastOutput_version
with the version information:

<BlastOutput_version>BLASTP 2.2.18+</BlastOutput_version>

Traceback (most recent call last):
  File "blast2.py", line 7, in <module>
    for blast_record in blast_records:
  File "/usr/lib/python2.5/site-packages/Bio/Blast/NCBIXML.py", line 577, in
    expat_parser.Parse(text, False)
  File "/usr/lib/python2.5/site-packages/Bio/Blast/NCBIXML.py", line 98, in
    eval("self.%s()" % method)
  File "<string>", line 1, in <module>
  File "/usr/lib/python2.5/site-packages/Bio/Blast/NCBIXML.py", line 216, in
    self._header.date = self._value.split()[2][1:-1]
IndexError: list index out of range

I've worked around this bug for now by commenting out the
offending line and setting the date to an empty string:

    def _end_BlastOutput_version(self):
        """version number of the BLAST engine (e.g., 2.1.2)

        Save this to put on each blast record object
        self._header.version = self._value.split()[1]
        # self._header.date = self._value.split()[2][1:-1]
        self._header.date = ''

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