[BioPython] NCBIXML - Blast in- and output

[Peter]

Hi again Björn,

> Now i was able to backtrace, where the Problem comes from. It may not be
> related to 32/64 Bit. It happens when Blast's calculation
> of the "Karlin-Altschul parameters" fails. This may happen due low
> complexity of the Query sequence (see Blast FAQ).
> I've attached a tar with the Blast-output and the reference and input
> files. I didn't stumble over this problem before on 32 Bit,
> because that was a smaller Sequenze-DB for testing purposes

It does sound like its nothing to do with 32bit versus 64bit.

Could you file a bug and then attach the following files
- reference.fasta
- input2.fasta
- output XML file (or say if its empty)

Using Blast 2.2.16, I got an empty output file (with messages "Could
not calculate ungapped Karlin-Altschul parameters due to an invalid
query sequence or its translation. Please verify the query sequence(s)
and/or filtering options" on the error stream).

Using Blast 2.2.10, I got XML output including messages like
"BlastKarlinBlkGappedCalc: Gap existence and extension values of -1
and -1 not supported for PAM250" (also on the error output).

This was on a 64bit Linux machine.  You haven't said what version of
standalone Blast you have - as you can see it does make a difference.

Peter