[Biopython-dev] [Bug 2529] NCBI BLAST XML parser does not support the online blast version 2.2.18+

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed Jun 25 16:24:45 UTC 2008


lordnapi at gmail.com changed:

           What    |Removed                     |Added
             Status|NEW                         |RESOLVED
         Resolution|                            |WORKSFORME

------- Comment #1 from lordnapi at gmail.com  2008-06-25 12:24 EST -------
The problem was caused by not having data in <BlastOutput_version>BLASTP
2.2.18+</BlastOutput_version> in the XML files. I fixed the problem for myself
by changing _end_BlastOutput_version function in the Blast/NCBIXML.py file to
the following (starts at line 208). I still don't know if having date is
important elsewhere.

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._valuesplit = self._value.split()
    self._header.version = self._valuesplit[1]
    if len(self._valuesplit) > 2 :
        self._header.date = self._value.split()[2][1:-1]
        self._header.date = ''

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