[Biopython-dev] [Bug 3037] PhyloXMLIO creates extremely ugly xml

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=3037





------- Comment #1 from eric.talevich at gmail.com  2010-03-27 22:58 EST -------
(In reply to comment #0)
> This is a request for an enhancement.
> 
> The xml code PhyloXMLIO creates has no linefeeds.  It would be very helpful for
> debugging if the XML is prettyprinted.
> 

This is a shortcoming of the ElementTree module in the Python standard library
-- the writer doesn't have an option for setting whitespace. But I agree it
would be nice to have this feature, so I'll leave the bug open as a reminder to
look for other ways to do this.

In the meantime I recommend using some external tool to reformat the XML if you
want to look at the raw data. XML Starlet can do this:
http://xmlstar.sourceforge.net/


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