[Biopython-dev] Parsing RPS-Blast output with BioPython
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.
MOAC Doctoral Training Centre
University of Warwick, UK
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