On Thu, Feb 16, 2012 at 9:02 PM, Peter wrote:
> On Thu, Feb 16, 2012 at 6:42 PM, Chris wrote:
>> On Feb 16, 2012, at 12:24 PM, Peter wrote:
>>> I also need to look at merging multiple BLAST XML outputs,
>>> but this is looking promising.
>> Yep, that's definitely one where a simple concatenation
>> wouldn't work (though NCBI used to think so, years ago…)
> Well, given the NCBI's historic practise of producing 'XML'
> output which was the concatenation of several XML files,
> some tools will tolerate this out of practicality - the Biopython
> BLAST XML parser for example.
> But yes, some care is needed over the header/footer to
> ensure a valid XML output is created by the merge. This
> may also require renumbering queries... I will check.

Basic BLAST XML merging implemented and apparently working:

This does not currently attempt to remap the iteration
numbers or automatically assigned query names, e.g.
you can have this kind of thing in the middle of the XML
at a merge point:


That isn't a problem for some tools, e.g. my code in
Galaxy to convert BLAST XML to tabular, but I suspect
it could cause trouble elsewhere. If anyone has specific
suggestions for what to test, that would be great.

If this is an issue, then the merge code needs a little
more work to edit these values.

I think the FASTA split code could be reviewed for
inclusion though. Dan - do you want to look at that?
Would a clean branch help?


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