[BioPython] Blast parser error

[Jeffrey Chang]

It is likely because the BLAST format has changed.  If you can send the 
BLAST output file that is causing the problem, I can take a look at it 
for you.  Otherwise, you will need to figure out which line is causing 
the problem and update the parser to deal with it properly.

Jeff



On Mar 14, 2004, at 7:47 PM, Maqbool, Nauman wrote:

> 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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