[BioPython] Blast parser error

Maqbool, Nauman nauman.maqbool at agresearch.co.nz
Sun Mar 14 22:47:37 EST 2004


Hi 

I am new to biopython and am trying out the NCBI Standalone Blast
parser. While trying the blast parsing methods from the cookbook
(parsing standalone Blastn output) I got the following error message:

>>> ================================ RESTART
================================
>>> 

Traceback (most recent call last):
  File "C:/Python/NM Python work/SV/sing_blst_SVparse.py", line 26, in
-toplevel-
    testparser(in_file)
  File "C:/Python/NM Python work/SV/sing_blst_SVparse.py", line 11, in
testparser
    b_record = b_iterator.next()
  File "C:\Python23\Lib\site-packages\Bio\Blast\NCBIStandalone.py", line
1332, in next
    return self._parser.parse(File.StringHandle(data))
  File "C:\Python23\Lib\site-packages\Bio\Blast\NCBIStandalone.py", line
557, in parse
    self._scanner.feed(handle, self._consumer)
  File "C:\Python23\Lib\site-packages\Bio\Blast\NCBIStandalone.py", line
97, in feed
    self._scan_rounds(uhandle, consumer)
  File "C:\Python23\Lib\site-packages\Bio\Blast\NCBIStandalone.py", line
153, in _scan_rounds
    self._scan_alignments(uhandle, consumer)
  File "C:\Python23\Lib\site-packages\Bio\Blast\NCBIStandalone.py", line
287, in _scan_alignments
    self._scan_pairwise_alignments(uhandle, consumer)
  File "C:\Python23\Lib\site-packages\Bio\Blast\NCBIStandalone.py", line
297, in _scan_pairwise_alignments
    self._scan_one_pairwise_alignment(uhandle, consumer)
  File "C:\Python23\Lib\site-packages\Bio\Blast\NCBIStandalone.py", line
309, in _scan_one_pairwise_alignment
    self._scan_hsp(uhandle, consumer)
  File "C:\Python23\Lib\site-packages\Bio\Blast\NCBIStandalone.py", line
337, in _scan_hsp
    self._scan_hsp_alignment(uhandle, consumer)
  File "C:\Python23\Lib\site-packages\Bio\Blast\NCBIStandalone.py", line
368, in _scan_hsp_alignment
    read_and_call(uhandle, consumer.query, start='Query')
  File "C:\Python23\Lib\site-packages\Bio\ParserSupport.py", line 300,
in read_and_call
    raise SyntaxError, errmsg
SyntaxError: Line does not start with 'Query':
ncbiClient.20040311_1242_9391.log

>>> 

The version of Blast we are running is: 2.2.6 [Apr-09-2003]. I found a
similar blast parser error in the biopython archives but that was
referring to the output format change in blastx. I don't think that the
Blastn output has changed in the recent past, so it might be due to
something that I might be missing in my script, here is the script that
I am running:


from Bio.Blast import NCBIStandalone

in_file = 'test.blast'

def testparser(blastfile):
    blast_out = open(blastfile, "r")
    b_parser = NCBIStandalone.BlastParser()
    b_iterator = NCBIStandalone.Iterator(blast_out, b_parser)

    while 1:
        b_record = b_iterator.next()

        if b_record is None:
            break

        E_VALUE_THRESH = 0.05
        for alignment in b_record.alignments:
            for hsp in alignments.hsp:
                if hsp.expect < E_VALUE_THRESH:
                    print '*****Alignmnent*****'
                    print 'sequence:', alignment.title
                    print 'length:', alignment.length
                    print 'e value:', hsp.expect

# Main
testparser(in_file) 


Any help will be highly appreciated.

Regards

Nauman

********************************************
Nauman J Maqbool PhD
Bioinformatics Group
AgResearch Invermay
Private Bag 50034
Puddle Alley
Mosgiel
New Zealand
email: nauman.maqbool at agresearch.co.nz
Tel: +64-3-489 9031
Fax: +64-3-489 3739
********************************************

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