[BioPython] Problem with BLAST parser in NCBIStandalone

[Jeffrey Chang]

It looks like the format has changed a little bit.  Try this patch and
let me know if this doesn't fix the problem.

Jeff


*** NCBIStandalone.py.orig      2002-03-18 13:46:08.056022000 -0800
--- NCBIStandalone.py   2002-05-08 22:25:44.664509000 -0700
***************
*** 199,205 ****
          # indicates that no descriptions follow, and we should go straight
          # to the alignments.
          if not attempt_read_and_call(
!             uhandle, consumer.description_header, contains='Score     E'):
              # Either case 2 or 3.  Look for "No hits found".
              attempt_read_and_call(uhandle, consumer.no_hits,
                                    contains='No hits found')
--- 199,206 ----
          # indicates that no descriptions follow, and we should go straight
          # to the alignments.
          if not attempt_read_and_call(
!             uhandle, consumer.description_header,
!             has_re=re.compile(r'Score {4,5}E')):
              # Either case 2 or 3.  Look for "No hits found".
              attempt_read_and_call(uhandle, consumer.no_hits,
                                    contains='No hits found')


On Thu, May 09, 2002 at 12:21:18PM +1000, Chris Francis wrote:
> 
> 
> Running a blast locally (BLASTP 2.2.3):
> 
> blastall -p blastp -d nr.seq -i TyrR.fasta -o TyrR2.out
> 
> The resulting file format was unable to be parsed by 
> NCBIStandalone.BlastParser, giving the previously posted error.
> 
> I have attached the output, as requested.
> 
> Thank-you for looking into this.
> 
> C.Francis
> 
> 
> 
> 
> 
> 
> _________________________________________________________________
> Send and receive Hotmail on your mobile device: http://mobile.msn.com