[BioPython] Blast Parser Dies

[Jeffrey Chang]

The format has changed in a way that the parser does not accept.  Can
you please send the output file?

Jeff



On Thu, Jan 30, 2003 at 05:19:54PM -0700, Naveed Iqbal wrote:
> Hey does anybody know what going wrong here?
> 
> from Bio.Blast import NCBIStandalone
> 	
> blast_db  		   = "E:\\blast\\protein"
> blast_file		   = "E:\\blast\\test.txt"
> blast_exe 		   = "E:\\blast\\blastall.exe"
> 
> blast_out,error_info =
> NCBIStandalone.blastall(blast_exe,'blastp',blast_db,blast_file)
> b_parser    	   = NCBIStandalone.BlastParser()
> b_record    	   = b_parser.parse(blast_out) # This is where it dies
> 
> The error message
> ----------------
> File "E:\Python22\blast.py", line 20, in ?
>     b_record     =  b_parser.parse(blast_out)
>   File "E:\Python22\Lib\site-packages\Bio\Blast\NCBIStandalone.py", line
> 515, in parse
>     self._scanner.feed(handle, self._consumer)
>   File "E:\Python22\Lib\site-packages\Bio\Blast\NCBIStandalone.py", line
> 85, in feed
>     self._scan_database_report(uhandle, consumer)
>   File "E:\Python22\Lib\site-packages\Bio\Blast\NCBIStandalone.py", line
> 384, in _scan_database_report
>     read_and_call(uhandle, consumer.database, start='  Database')
>   File "E:\Python22\Lib\site-packages\Bio\ParserSupport.py", line 331,
> in read_and_call
>     raise SyntaxError, errmsg
> SyntaxError: Line does not start with '  Database'
> 
> 
> Any help would be greatly appreciated
> 
> Naveed Iqbal
> Dept. of Computer Science
> University of Colorado-Boulder
> 
> 
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