[BioPython] Problem with blastx output parsing =~
Peter
biopython at maubp.freeserve.co.uk
Wed Jun 13 10:30:20 UTC 2007
To update anyone not following bug 2090, I have updated the CVS copy of
Bio/Blast/NCBIStandalone.py to do a better job of recent plain text
Blast output. It can now parse the two BLASTX 2.2.15 files Italo sent me.
If anyone want to try this code, you can either update your entire
Biopython installation to CVS, or simply update the file
Bio/Blast/NCBIStandalone.py in your python site-packages directory
(after making a backup). You can get the latest version here:
http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/Blast/NCBIStandalone.py?cvsroot=biopython
You want the latest revision, 1.66 (the web interface is normally
updated within the hour).
Italo - please could we use those two files as test cases to include
with Biopython? And do let me know if any of your other 24,000 examples
fails.
Peter
P.S. Biopython can currently only cope with single query plain text
output from Blast. We recommend using the XML output.
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