[Biopython-dev] Blast XML Parse Improvements

[Fields, Christopher J]

Keep in mind there are significant changes for BLAST+ XML output in the latest release, not all of them good IMHO.  Peter has a pretty good writeup on this:

http://blastedbio.blogspot.com/2015/07/blast-xml-2-include-trouble.html

chris

On Jul 29, 2015, at 12:21 AM, Wibowo Arindrarto <w.arindrarto at gmail.com<mailto:w.arindrarto at gmail.com>> wrote:

Hi Travis,

There hasn't been any new test cases added for BLAST 2.2.30, as I
recall. Did you get the same behavior when using Bio.SearchIO to parse
it?

Best regards,
Bow

On Wed, Jul 29, 2015 at 7:12 AM, Travis Wrightsman <twrig002 at ucr.edu<mailto:twrig002 at ucr.edu>> wrote:
Biopython Devs,

I was trying to parse through a tblastn XML output with multiple queries in
the query file and it was generating a BLAST record object for each contig
in the subject file instead of each run. Is this the intended behavior or
has this not been updated for ncbi tools 2.2.30?

If it needs to be updated or finished, I'm more than happy to rewrite or
update some of the code in NCBIXML for the latest version.

-Travis

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