[Biopython] Problems parsing with PSIBlastParser
Miguel Ortiz Lombardia
ibdeno at gmail.com
Mon Oct 12 08:11:38 UTC 2009
Dear list members,
I have 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.
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.
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)
Anyone has a clue?
Thank you!
-- Miguel
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