[BioPython] Iterating over Blast file

[Sameet Mehta]

Hi all,
I have a blast output file.  I want to iterate over the results, Now i am 
doing the following

>>> from Bio.Blast import NCBIStandalone
>>> infile = open(r'C:\Sameet\only2blast.txt', 'r')
>>> parser = NCBIStandalone.BlastParser()
>>> iterator = NCBIStandalone.Iterator(infile, parser)
>>> while 1:
	record = iterator.next()
	if record is None:
		break
	for alignment in record.alignments:
		for hsp in alignments.hsps:
			if hsp.expect < 0.000000001:
				print alignment.title, hsp.sbjct_start

The code taken as is from the tutorial
I am getting the following trace

Traceback (most recent call last):
  File "<pyshell#12>", line 2, in -toplevel-
    record = iterator.next()
  File "C:\Python23\lib\site-packages\Bio\Blast\NCBIStandalone.py", line 
1378, in next
    return self._parser.parse(File.StringHandle(data))
  File "C:\Python23\lib\site-packages\Bio\Blast\NCBIStandalone.py", line 
603, in parse
    self._scanner.feed(handle, self._consumer)
  File "C:\Python23\lib\site-packages\Bio\Blast\NCBIStandalone.py", line 93, 
in feed
    read_and_call_until(uhandle, consumer.noevent, contains='BLAST')
  File "C:\Python23\Lib\site-packages\Bio\ParserSupport.py", line 335, in 
read_and_call_until
    line = safe_readline(uhandle)
  File "C:\Python23\Lib\site-packages\Bio\ParserSupport.py", line 411, in 
safe_readline
    raise SyntaxError, "Unexpected end of stream."
SyntaxError: Unexpected end of stream.

Now i have downloaded the latest version of the NCBIStandalone as advised by 
Jeff.  The module is working fine.  I can get the individual blast results 
one by one using the 'iterator.next()' command.  But when i have a big file, 
with 4 reports one after the other.  I get this error.  Now I see that there 
is no problem with the NCBIStandalone, however, i dont know if i am diong 
anything wrong.  As far as the tutorial is concerned, i am following it to 
the line.

regards
Sameet
--
National Centre for Cell Science, Pune