[Biopython] Problems parsing with PSIBlastParser
biopython at maubp.freeserve.co.uk
Mon Oct 12 05:19:33 EDT 2009
On Mon, Oct 12, 2009 at 9:11 AM, Miguel Ortiz Lombardia
<ibdeno at gmail.com> wrote:
> Dear list members,
> I have a problem with NCBIStandalone.PSIBlastParser, which I need to use
> instead of NCBIXML since the latter one lacks some record properties that I
> My code used to work until recently (say three months) and now it seems
> something has changed in the latest biopython (1.52-1, I install it on an
> intel OSX 10.5.8 via fink). I get the same problem irrespectively of whether
> I use python 2.5 or 2.6.
You definitely didn't upgrade your copy of BLAST at the same time?
Could you file a bug please. Then run PSI-BLAST "by hand" and
record the plain text output to a file, and upload the file to Bugzilla.
Note you have to file the bug before it will let you upload a file. Having
the XML output could be helpful too.
Also, can we use your BLAST file as a unit test?
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