I process my blast (BLASTN 2.2.26+) searches through a script that divides the fasta inputs into N pieces, distributes one blast instance for each piece (in N processes), and, once over, concatenates the outputs into one file. It works pretty well with the table output format, but what about the xml? Indeed, I want to test a software that takes as input only xml format (a dummy cat does not work), and I'm struggling with that case.
Have you an idea on how to make one consistant xml output from several (it can be hundreds) "sub-"outputs? (I need a biopython NCBIXML parsability) ;-) ).