[Bioperl-l] Bio::SeqIO::tinyseq

Heikki Lehvaslaiho heikki at ebi.ac.uk
Wed Jan 28 09:54:56 EST 2004


The more I use XML the more pragmatic I get. When things get tight, I've used 
perl directly to modify XML files; and gained 10x speed increase. Validation 
in most cases is not practical, so would not  worry too much about about it, 

BTW, I am now convinced that structure definitions for any database-related 
format should be constructed from several definitions; in this case, one for 
top level and an other for the entry level.

Thanks for pointing out that new line character in my code. 


On Wednesday 28 Jan 2004 11:24, Dave Howorth wrote:
> Heikki Lehvaslaiho wrote:
> > The best way to do this is to ignore the root level of the xml, use perl
> > to parse entries out of it, and pass entry xml only to the parser. This
> > keeps the memory usage down and you can parse as large file as you want.
> Hmmm, it may be pragmatic but I'm sure there are other meanings of
> 'best'.  By throwing away the root level you're losing any chance to
> validate the document or use other XML tools and you run the risk of
> making assumptions ...
> >     local $/ = "</seqDiff>\n";
> ... There's no reason to expect there will ALWAYS be a newline following
> the tag in a valid XML file (suppose it's created by some XSLT tool that
> cares nothing about readability).  You're making an assumption above and
> beyond the specification about how the XML is represented.
> Cheers, Dave
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     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
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