[Biopython] Legacy blast XML parser returns prematurely StopIteration

[Peter Cock]

On Wed, May 16, 2012 at 10:32 AM, Martin Mokrejs
<mmokrejs at fold.natur.cuni.cz> wrote:
> Hi,
>  I am parsing some blast 2.2.24 XML output and the last record I get is the one from
> iteration 124. I see that entry is followed by a new <Iteration_iter-num> section which
> is probably the culprit. I will try newer legacy blast but still, biopython could maybe
> overcome this bug in XML input?
>
> blastall -p blastn -A 4 -i SRR068315.fasta -d my_targets.fasta -F 0 -S 1 -r 2 -e 10e-30 -m 7
>

Could you file a bug here and attach the complete XML test case please?
http://redmine.open-bio.org/projects/biopython

Our XML parser should handle both NCBI  'legacy' BLAST and BLAST+

Thanks,

Peter