[BioPython] NCBIStandalone Parser problem

[Michiel Jan Laurens de Hoon]

Could you try this again with Biopython version 1.40b and see if the problem 
still occurs there? If so, could you send me the query that you are using so I 
can replicate this error?

--Michiel.

edeveaud at pasteur.fr wrote:

> 	Hi,
> 	
> I just wanted to mention a problem with the NCBIStandalone Parser 
> 
> when I try to parse a blast nucleic report file with No hits found 
> using the following code (reduced to the minimum)
> 
> 
> saint-moret:~ > cat blast_pb.py
> #! /local/cours/bin/python
> from Bio.Blast import NCBIStandalone
> import sys
> 
> blast_bin='/local/cours/bin/blastall'
> blast_prog = 'blastn'
> blastDB='/local/cours/bank/test_db'
> query = sys.argv[1]
> 
> # blast exec
> OUT, ERR = NCBIStandalone.blastall(blast_bin, blast_prog, blastDB, query)
> 
> # parser instanciation
> parser=NCBIStandalone.BlastParser()
> 
> # parsing
> record = parser.parse(OUT)
> 
> 
> 
> execution fails with the following traceback
> saint-moret:~ > ./blast_pb.py query2
> Traceback (most recent call last):
>   File "./blast_pb.py", line 17, in ?
>     record = parser.parse(OUT)
>   File "/local/cours/lib/python2.3/site-packages/Bio/Blast/NCBIStandalone.py",
> line 567, in parse
>     self._scanner.feed(handle, self._consumer)
>   File "/local/cours/lib/python2.3/site-packages/Bio/Blast/NCBIStandalone.py",
> line 95, in feed
>     self._scan_header(uhandle, consumer)
>   File "/local/cours/lib/python2.3/site-packages/Bio/Blast/NCBIStandalone.py",
> line 129, in _scan_header
>     read_and_call_while(uhandle, consumer.noevent, blank=1)
>   File "/local/cours/lib/python2.3/site-packages/Bio/ParserSupport.py", line
> 314, in read_and_call_while
>     line = safe_readline(uhandle)
>   File "/local/cours/lib/python2.3/site-packages/Bio/ParserSupport.py", line
> 411, in safe_readline
>     raise SyntaxError, "Unexpected end of stream."
> SyntaxError: Unexpected end of stream.
> 
> blast manualy run give me the following results
> 
> 
> 
> saint-moret:~ > blastall -p blastn -d /local/bank/hpylori/blast2/hp26695_genome
> -i query2
> BLASTN 2.2.10 [Oct-19-2004]
> 
> 
> Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
> Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
> "Gapped BLAST and PSI-BLAST: a new generation of protein database search
> programs",  Nucleic Acids Res. 25:3389-3402.
> 
> Query= no_hits
>          (120 letters)
> 
> Database: Hpylori 
>            1 sequences; 1,667,867 total letters
> 
> Searching[NULL_Caption] WARNING:  [000.000]  no_hits: SetUpBlastSearch failed.
> [NULL_Caption] ERROR:  [000.000]  no_hits: BLASTSetUpSearch: Unable to
> calculate Karlin-Altschul params, check query sequence
> [NULL_Caption] ERROR:  [000.000]  no_hits: BLASTSetUpSearch: Unable to
> calculate Karlin-Altschul params, check query sequence
> done
> 
>  ***** No hits found ******
> 
>   Database: Hpylori
>     Posted date:  May 3, 2004  3:55 AM
>   Number of letters in database: 1,667,867
>   Number of sequences in database:  1
>   
> Lambda     K      H
>    -1.00    -1.00    -1.00 
> 
> 
> 
> 
> the parser works perfectly with blastn reports with hits.
> we discover the problem, trying to work on a blast report of multiple sequences
> versus one bank using the NCBIStandalone.iterator.
> 
> some details
> running Python 2.3.4, Biopython 1.30 and blastall 2.2.10 Release on MacOSX 
> 
> 	thank's for any information 
> 
> 	Eric
> 
> _______________________________________________
> BioPython mailing list  -  BioPython at biopython.org
> http://biopython.org/mailman/listinfo/biopython
> 
> 

-- 
Michiel de Hoon, Assistant Professor
University of Tokyo, Institute of Medical Science
Human Genome Center
4-6-1 Shirokane-dai, Minato-ku
Tokyo 108-8639
Japan
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon