[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





------- Comment #2 from ngcrawfo at bu.edu  2008-10-27 16:24 EST -------
Peter,

Thanks for the insight.  I'll mess about with the gap and existence parameters.
 Thanks again!

- Nick

(In reply to comment #1)
> 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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