[Biopython-dev] Re: Blast parser

Jeffrey Chang jchang at SMI.Stanford.EDU
Thu Sep 27 19:16:15 EDT 2001

Great!  Thanks a lot.  The patch looks good really good.  The only 
thing is, can you change the try: except: to an explicit test for the 
end of the stream?  That would be more robust to changes in the error 

             read_and_call(uhandle, consumer.blast_cutoff, start='S2')
         except SyntaxError, reason:
             assert str(reason) == "Unexpected end of stream.", \
               "Unexpected reason: '%s'" % reason


if uhandle.peekline():
   attempt_read_and_call(uhandle, consumer.blast_cutoff, start='S2')


At 5:02 PM -0400 9/27/01, Brad Chapman wrote:
>Hi Jeong;
>I'm ccing this message to biopython-dev at biopython.org. By the way,
>asking your questions there is probably a better place than asking
>me directly, as there are lots of people there to help.
>>  Hello, I would like to know if the blast standalone parser supports parsing
>>  of the BLASTX results. When I use blast standalone parser to parse BLASTX
>>  results, I get an error message of the following:
>>  SyntaxError: Line does not start with 'length of query':
>>  length of database: 27,975,647
>Yup, it looks like the blastx output format has changed somewhat
>since the last time it was used/tested with blastx. The specific
>things that have changed are the lack of the following lines in
>blastx output:
>'length of query'
>'effective length of query'
>'effective search space:'
>I've fixed Bio/Blast/NCBIStandalone.py so that it works again on
>blastx. The diff to this file is attached. Jeff, if you have a
>chance could you give me the okay on this before I check it in? The
>current regression tests all pass with these changes. When I check
>it in, I can also add the blastx example file I used to fix this.
>Jeong, thanks for the bug report! Please let us know if this fix
>doesn't get things working again for you.
>PGP public key available from http://pgp.mit.edu/
>Attachment converted: Macintosh HD:NCBIStandalone.py.diff 
>(TEXT/text) (0015B4C0)

More information about the Biopython-dev mailing list