[BioPython] NCBIStandalone Parser problem

[edeveaud at pasteur.fr]

	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