[Biopython-dev] [Bug 2927] New: Problem parsing PSI-BLAST plain text output with NCBStandalone.PSIBlastParser

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2927

           Summary: Problem parsing PSI-BLAST plain text output with
                    NCBStandalone.PSIBlastParser
           Product: Biopython
           Version: 1.52
          Platform: Macintosh
        OS/Version: Mac OS
            Status: NEW
          Severity: blocker
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: ibdeno at gmail.com


This is a problem with NCBIStandalone.PSIBlastParser, which I need to use
instead of NCBIXML since the latter one lacks some record properties that I
need.

My code used to work until recently (say three months) and now it seems
something has changed in the latest biopython (1.52-1, I install it on an intel
OSX 10.5.8 via fink). I get the same problem irrespectively of whether I use
python 2.5 or 2.6 and also the same for blastpgp 2.2.18 and 2.2.22

Here follows the relevant part of the code:

####

   blast_out, error_info = NCBIStandalone.blastpgp(
       blastcmd='/usr/local/blast-2.2.18/bin/blastpgp',
       database='/opt/BlastDBs/' + db,
       infile=file,
       npasses=passes,
       program='blastpgp',
       descriptions='500',
       alignments='1000',
       align_view='0',
       matrix_outfile=outbase + '.' + db + '.' + str(passes) + '.pssm')

   b_parser = NCBIStandalone.PSIBlastParser()

   b_record = b_parser.parse(blast_out)

####

And this is the error that I now get:

####

 File "/Users/mol/bin/lpbl.py", line 64, in doblast
   b_record = b_parser.parse(blast_out)
 File "/sw/lib/python2.6/site-packages/Bio/Blast/NCBIStandalone.py", line 777,
in parse
   self._scanner.feed(handle, self._consumer)
 File "/sw/lib/python2.6/site-packages/Bio/Blast/NCBIStandalone.py", line 97,
in feed
   self._scan_rounds(uhandle, consumer)
 File "/sw/lib/python2.6/site-packages/Bio/Blast/NCBIStandalone.py", line 234,
in _scan_rounds
   self._scan_alignments(uhandle, consumer)
 File "/sw/lib/python2.6/site-packages/Bio/Blast/NCBIStandalone.py", line 376,
in _scan_alignments
   self._scan_pairwise_alignments(uhandle, consumer)
 File "/sw/lib/python2.6/site-packages/Bio/Blast/NCBIStandalone.py", line 386,
in _scan_pairwise_alignments
   self._scan_one_pairwise_alignment(uhandle, consumer)
 File "/sw/lib/python2.6/site-packages/Bio/Blast/NCBIStandalone.py", line 398,
in _scan_one_pairwise_alignment
   self._scan_hsp(uhandle, consumer)
 File "/sw/lib/python2.6/site-packages/Bio/Blast/NCBIStandalone.py", line 433,
in _scan_hsp
   self._scan_hsp_alignment(uhandle, consumer)
 File "/sw/lib/python2.6/site-packages/Bio/Blast/NCBIStandalone.py", line 464,
in _scan_hsp_alignment
   read_and_call(uhandle, consumer.query, start='Query')
 File "/sw/lib/python2.6/site-packages/Bio/ParserSupport.py", line 303, in
read_and_call
   method(line)
 File "/sw/lib/python2.6/site-packages/Bio/Blast/NCBIStandalone.py", line 1138,
in query
   raise ValueError("I could not find the query in line\n%s" % line)
ValueError: I could not find the query in line
Query: 0    -

####

Now, the interesting thing is that if I run blastpgp directly and catch the
output to a file, this file never includes such a line as:

Query: 0    -

Actually, if I modify my code so it reads this output file, the PSIBlastParser
processes it without error.

Not sure if this is relevant, but I have found that something may have changed
in NCBIStandalone recently, namely, this bit:

   _query_re = re.compile(r"Query(:?) \s*(\d+)\s*(.+) (\d+)")
   def query(self, line):
       m = self._query_re.search(line)
       if m is None:
           raise ValueError("I could not find the query in line\n%s" % line)

I will post log files in plain text and xml after submitting this bug report.


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