[Biopython-dev] [Bug 2634] PAM30 Matrix doesn't work with qblast

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2634


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
            Summary|PAM30 Matrix doesn't work   |PAM30 Matrix doesn't work
                   |with                        |with qblast




------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2008-10-27 16:14 EST -------
The error from Biopython is because it can't find the RID and RTOE references
in what is normally a "please wait" HTML page.  The reason being you have
triggered an error.  From dumping the HTML requested:

-------------------------------
Message ID#33 Error: Cannot validate the Blast options:  Gap existence and
extension values of 11 and 1 not supported for PAM30
supported values are:
32767, 32767
7, 2
6, 2
5, 2
10, 1
9, 1
8, 1

This error message indicates that the combination of options for this Blast
search is inconsistent or invalid. This can happen when the selected Blast
program does not support one of the options provided, when two or more options
have conflicting values, etc. If you are using URL API, please check the
options mentioned in the error message string and re-submit your search. Please
note that the current version of the Blast CGI application is stricter at
validating Blast options than it has been historically. If this error persists,
please, contact <a
href="mailto:blast-help at ncbi.nlm.nih.gov">Blast-help at ncbi.nlm.nih.gov</a> for
more help.
-------------------------------

Short of printing out the whole HTML dump, I'm not sure how best to tell the
user about this kind of error - automatically extracting the error message
looks unreliable.

In anycase, I think you need to investigate the gap options and see if you can
match what you are trying to mimic.

Peter


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