[BioPython] Bio.Blast.NCBIWWW.blast returns before search is complete

[Iddo Friedberg]

Noah,

Thanks for your interest in our project. We are aware of this bug, which 
has already been fixed in CVS, and we are rolling Biopython 1.40 
tomorrow, hopefully. The cookbook example is kinda out of date: the 
blast method is deprecated, NCBIWWW uses qblast now.

If you can wait for a couple of days, we would have Biopython 1.40 out. 
If you want to live on the bleeding edge, check out a copy fom CVS. Go 
to: http://biopython.org/CVS and read there on how to do it.

Not that the blast method is deprecated, and qblast is being used now. 
However, qblast is only in the CVS version, not in the 1.30 release.

HTH,

Iddo

Noah Hoffman wrote:

>Hello biopython list -
>
>This is my first attempt to use the biopython tools, so I thought I'd
>check with the mailing list first before submitting it as a bug to see
>if I'm missing something obvious (I wouldn't be surprised!). I'm
>running Biopython version 1.30 on mac os 10.3.8, python version 2.3.
>
>Just doing a simple blast search, following the example in the
>cookbook. The job is dispatched properly, and often (but not always)
>returns the "search pending" message rather than the search results
>itself. I believe that I've found the code in Bio/Blast/NCBIWWW.py
>responsible for the failure to wait for the results to be ready on the
>NCBI end - it actually looks like the python code is correct, and that
>the server is supplying misleading data (held in the "comment"
>variable below).
>
>Code snippets from the module with my debugging code (flagged by ####
>NH) follows:
>
>% cat -n /System/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site-packages/Bio/Blast/NCBIWWW.py
>| grep -A3 -B3 "#### NH"
>
>   769      while 1:
>   770          # pause before trying to get the results
>   771
>   772          print '(line %s) pausing: refresh_delay = %s' %
>(line_no(), refresh_delay)  #### NH
>   773
>   774          time.sleep(refresh_delay)
>   775
>--
>   783          ready, results_cgi, results_params =
>_parse_blast_results_page(handle)
>   784
>   785          print '(line %s) checking search status; ready = %s' \
>   786          % (line_no(), ready) #### NH
>   787
>   788          results_params['FORMAT_TYPE']=format_type
>   789          results_params['NCBI_GI']='yes'
>--
>   869              # //--></SCRIPT>
>   870              comment = string.lower(comment)
>   871
>   872              print '(line %s) comment:\n--->%s<---' %
>(line_no(),comment.strip()) #### NH
>   873
>   874              if string.find(comment, 'status=ready') >= 0:
>   875                  self.ready = 1
>--
>   982          outhandle.write(data)
>   983      sock.close()
>   984
>   985  def line_no(): #### NH
>   986          import inspect
>   987          try: raise AttributeError
>   988          except AttributeError: return inspect.stack()[1][2]
>
>... and the output resulting from the dispatch of two sequence files,
>445.fasta and 457.fasta:
>
>searching 445.fasta against the nr database using tblastn
>(line 772) pausing: refresh_delay = 56
>(line 872) comment:
>--->qblastinfobegin
>        status=waiting
>qblastinfoend<---
>(line 872) comment:
>--->settimeout('document.forms[0].submit();',11000);
>//<---
>(line 785) checking search status; ready = 0
>(line 772) pausing: refresh_delay = 56
>(line 872) comment:
>--->qblastinfobegin
>        status=waiting
>qblastinfoend<---
>(line 872) comment:
>--->settimeout('document.forms[0].submit();',12000);
>//<---
>(line 785) checking search status; ready = 0
>(line 772) pausing: refresh_delay = 56
>(line 872) comment:
>--->qblastinfobegin
>        status=ready
>qblastinfoend<---
>(line 785) checking search status; ready = 1
>writing 445_tblastn.html
>
>searching 457.fasta against the nr database using tblastn
>(line 772) pausing: refresh_delay = 39
>(line 872) comment:
>--->qblastinfobegin
>        status=waiting
>qblastinfoend<---
>(line 872) comment:
>--->settimeout('document.forms[0].submit();',17000);
>//<---
>(line 785) checking search status; ready = 0
>(line 772) pausing: refresh_delay = 39
>(line 872) comment:
>--->qblastinfobegin
>        status=waiting
>qblastinfoend<---
>(line 872) comment:
>--->settimeout('document.forms[0].submit();',17000);
>//<---
>(line 785) checking search status; ready = 0
>(line 772) pausing: refresh_delay = 39
>(line 872) comment:
>--->qblastinfobegin
>        status=ready
>qblastinfoend<---
>(line 785) checking search status; ready = 1
>writing 457_tblastn.html
>
>% du -h *tblastn.html
>4.0k    445_tblastn.html
>28k     457_tblastn.html
>
>As you can see from the file sizes, only the search using 457.fasta
>returned actual results, despite the fact that the while loop seemed
>to end appropriately once status=ready appeared in the comment
>variable.
>
>Anyone have any ideas? Is this simply erratic behavior by the NCBI
>server that we can not hope to have any control over? Is this a known
>problem that has been addressed in the CVS repository?
>
>Thanks a lot,
>Noah
>_______________________________________________
>BioPython mailing list  -  BioPython at biopython.org
>http://biopython.org/mailman/listinfo/biopython
>
>
>  
>


-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037 USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 713 9930
http://ffas.ljcrf.edu/~iddo
==========================
The First Automated Protein Function Prediction SIG
Detroit, MI June 24, 2005
http://ffas.burnham.org/AFP