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

Tim White w.t.white at massey.ac.nz
Sat Apr 23 08:33:53 EDT 2005

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,

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