[Biopython-dev] [Bug 2090] Blast.NCBIStandalone BlastParser fails with blastall 2.2.14

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2090





------- Comment #1 from grunberg at embl.de  2006-11-29 14:03 -------
Things get worse with the current blastall 2.2.15. _scan_parameters in
NCBIStandalone.py expects "Number of HSP's better" which in the later blastall
versions has changed to: "Number of sequences better".  
This prevents the parser from fetching the next two lines even though they
would be there and then we get exceptions etc. 

Another independent problem occurs further down -- The lines::
  T: 11
  A: 40
have now changed to::
  Neighboring words threshold: 11
  Window for multiple hits: 40
and again we run into an exeption. Both problems also concern in the latest CVS
snapshot.

Both can be fixed with some additional attempt_read_and_call but I am not sure
whether my quick and dirty fixes is following the right spirit...

change A:
---------
INSERT BEFORE...::
        # not in blastx 2.2.1
        attempt_read_and_call(uhandle, consumer.query_length,
                              has_re=re.compile(r"[Ll]ength of query"))
...These two statements::

        # in blastall 2.2.15
        attempt_read_and_call(uhandle, consumer.noevent,
                                 start="Number of HSP's gapped:")

        attempt_read_and_call(uhandle, consumer.noevent,
                          start="Number of HSP's successfully")

Change B:
---------
REPLACE::
        # not in BLASTN 2.2.9
        attempt_read_and_call(uhandle, consumer.threshold, start='T')
        read_and_call(uhandle, consumer.window_size, start='A')

BY::
        # not in BLASTN 2.2.9
        attempt_read_and_call(uhandle, consumer.threshold, start='T')
        attempt_read_and_call(uhandle, consumer.window_size, start='A')
        ## renamed in BLASTALL 2.2.15
        attempt_read_and_call(uhandle, consumer.threshold, start='Neighboring')
        attempt_read_and_call(uhandle, consumer.window_size, start='Window')

Could someone with more Biopython experience please validate and apply the fix?
THX!


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