[Biopython-dev] Parsing RPS-Blast output with BioPython

Peter biopython-dev at maubp.freeserve.co.uk
Wed Dec 8 10:09:52 EST 2004

As you might have noticed from the flood of emails onto the mailing list 
from the bugzilla-daemon (is this deliberate by the way?) I have done 
some more work on supporting the NCBI's (standalone) RPS-Blast program.


I have tested my changes with rpsblast 2.2.9 and 2.2.10 (which gives 
identical output except for the version number).

I have tested my changes do not alter the results of the existing test 
collection (bt001 to bt071) used by test_NCBIStandalone.py, and have 
submitted a new test file of rpsblast 2.2.10 output.

[So far all this was done on Windows, I am going to try and setup 
RPS-Blast on a linux machine as well]

So what happens now?

There doesn't seem to be any guidelines on the website for this...

e.g. preferred format of patches/diff files - my code is just an edited 
version of the current CVS copy of NCBIStandalone.py

Do I have to wave at the core-developers to give it the once over?

Or would someone else on the list volunteer to double check my changes 
seem to work on their system?  Ideally someone familiar with all the 
parameters for RPS-Blast, as I have just been using the default settings.

Thanks again

MOAC Doctoral Training Centre
University of Warwick, UK

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