[Bioclusters] blast output (-m 7) in XML, and the XML spec

[Joe Landman]

Hi Tim:

   I wanted to make sure my understanding of the standard was correct. 
I usually use xmllint to make sure a document is standard.

   The problem is that this is an issue with NCBI BLAST, and I haven't 
been too successful at get our patches included in the past, so I am 
hesitant to fix the code.  Might be easier to write a simple shoe-horn 
function to fix this (current plan) for the post-processing parser.  I 
will look at the xml out code and if we can fix it easily, and maintain 
the patch as we do for the Opteron bits, then we might do this.

   Thanks for your note on this.

Joe

Tim White wrote:
> The line:
> 
> <?xml version="1.0"?>
> 
> can appear only once in a well-formed XML file, right at the top.  Also,
> if a DOCTYPE tag appears, it must appear immediately after this tag
> (formally this is called a "document type declaration").  So it seems to
> me that you need to arrange for the second "<?xml...?>" tag to be
> removed, and for the "<!DOCTYPE...>" tag appearing after it to be either
> removed as well, or moved to just after the initial "<?xml...?>" tag.
> 
> I would not expect any XML parser to happily read your document as it
> stands, though of course some might.  (As an aside, the "culture"
> surrounding XML generally discourages leniency in parsing, in the hopes
> of ensuring that every XML document is well-formed, and will therefore
> be interpreted the same way by all XML tools.)
> 
> Hope this helps,
> Tim
> 
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Joseph Landman, Ph.D
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