[Biopython] Fwd: BlastParsing gives Value Error: Invalid header?

[Sarttu Bourvir]

Hi,
I am new to both python and biopython.
What I'm trying to do is to parse a blast result xml file (myblast.xml),
attached here.

The code looks like this:

#!/usr/bin/env python
import sys
import re
import Bio
from Bio.Blast import NCBIWWW
from Bio.Blast import NCBIXML
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Blast import NCBIStandalone


infile = raw_input ("which file:")
result_handle = open(infile,'r')
blast_parser = NCBIStandalone.BlastParser()
blast_iterator = NCBIStandalone.Iterator(result_handle, blast_parser)
blast_record = blast_iterator.next()
for blast_record in blast_iterator:
   E_VALUE_THRESH = 0.01
   for alignment in blast_records.alignments:
       for hsp in alignment.hsps:
           if hsp.expect < E_VALUE_THRESH:
               print '****Alignment****'
               print 'sequence', alignment.title
               print 'alignment length', alignment.length



When I try to run it,I get this:
Traceback (most recent call last):
 File "Blastparsee.py", line 17, in <module>
   blast_record = blast_iterator.next()
 File "/usr/lib/pymodules/python2.6/Bio/Blast/NCBIStandalone.py", line
1645, in next
   return self._parser.parse(File.StringHandle(data))
 File "/usr/lib/pymodules/python2.6/Bio/Blast/NCBIStandalone.py", line
804, in parse
   self._scanner.feed(handle, self._consumer)
 File "/usr/lib/pymodules/python2.6/Bio/Blast/NCBIStandalone.py", line
100, in feed
   self._scan_header(uhandle, consumer)
 File "/usr/lib/pymodules/python2.6/Bio/Blast/NCBIStandalone.py", line
225, in _scan_header
   raise ValueError("Invalid header?")
ValueError: Invalid header?


I attached the xml file I've been trying to blast. However, I get the same
error if I try using any other xml files from blast.
What's going on?

Thank you!
Cheers,
Sar

P.S. If this type of messages are not allowed on this e-mailing list I
apologize and promise to behave in the future!;)
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