[BioPython] Syntax error while parsing Blast output

[David Garfield]

Hey list,

    I'm having an issue with the BlastParser and Iterator from  
NCBIStandalone.  I assume its because NCBI has gone and changed the  
output file (again)...or I'm an idiot....but maybe there's a real  
problem here.


I'm trying to parse a blast result using the following code:

def filter_blast_results(blast_results, blast_cut_off):
	b_parser = NCBIStandalone.BlastParser()
	b_iterator = NCBIStandalone.Iterator(blast_results, b_parser)
	hit_results = {}
	while 1:
		b_record = b_iterator.next()
		if b_record is None:
			break
		header = b_record.Header.query
		temp = []
		for alignment in b_record.alignments:
			for hsp in alignment.hsps:
				if hsp.expect < blast_cut_off:
					temp.append(alignment.title)
		#we now remove duplicates from the temp list and add that the the  
hit_results
		hit_results[header] = remove_duplicates(temp)
	return hit_results

And I get the error I've included at the bottom of this message,  
something about "SyntaxError: Line does not start with 'Reference':"
I know that blast is working because I can print out what appears to  
my untrained eye to be a perfectly good XML of the results I see when  
I run blast manually.


Any help would be very much appreciated,

David



Traceback (most recent call last):
   File "test_scripts.py", line 7, in <module>
     single_blast_sequence.run_2way_blast('single_test_in.fasta','/ 
Users/dagarfield/urchins/blastdbs/urchin_2.0','/Users/dagarfield/ 
urchins/blastdbs/urchin_2.0','NA',.001,'/Users/dagarfield/urchins/ 
urchin_bin/blastall')
   File "/private/var/automount/Network/Share2/genomeScans/urchins/ 
alignment_methods/blast/single_blast_sequence.py", line 57, in  
run_2way_blast
     input_to_other_blast_matches = filter_blast_results 
(blast_results, blast_cut_off)
   File "/private/var/automount/Network/Share2/genomeScans/urchins/ 
alignment_methods/blast/single_blast_sequence.py", line 39, in  
filter_blast_results
     b_record = b_iterator.next()
   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/Bio/Blast/NCBIStandalone.py", line 1403, in next
     return self._parser.parse(File.StringHandle(data))
   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/Bio/Blast/NCBIStandalone.py", line 616, in parse
     self._scanner.feed(handle, self._consumer)
   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/Bio/Blast/NCBIStandalone.py", line 96, in feed
     self._scan_header(uhandle, consumer)
   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/Bio/Blast/NCBIStandalone.py", line 125, in  
_scan_header
     read_and_call(uhandle, consumer.reference, start='Reference')
   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/Bio/ParserSupport.py", line 300, in  
read_and_call
     raise SyntaxError, errmsg
SyntaxError: Line does not start with 'Reference':
   <BlastOutput_db>/Users/dagarfield/urchins/blastdbs/urchin_2.0</ 
BlastOutput_db>