[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
http://bugzilla.open-bio.org/show_bug.cgi?id=2527
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:
python-biopython-1.45-1.fc7
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
parse
expat_parser.Parse(text, False)
File "/usr/lib/python2.5/site-packages/Bio/Blast/NCBIXML.py", line 98, in
endElement
eval("self.%s()" % method)
File "<string>", line 1, in <module>
File "/usr/lib/python2.5/site-packages/Bio/Blast/NCBIXML.py", line 216, in
_end_BlastOutput_version
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 = ''
--
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.
More information about the Biopython-dev
mailing list