[BioPython] Blast parser error

[Maqbool, Nauman]

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
********************************************

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================