[Bioperl-l] HowTo:SearchIO

Chris Fields cjfields at uiuc.edu
Wed Feb 14 15:12:21 EST 2007


On Feb 14, 2007, at 12:55 PM, David Messina wrote:

>
> On Feb 14, 2007, at 11:28 AM, Chris Fields wrote:
>
>> I would also strongly encourage switching to using XML-based parsing,
>
> Unless anyone objects, I would be happy to update the HOWTO to
> suggest people make the switch and give an example of XML parsing.
>
> The Bio::SearchIO synopsis is already an XML example. However,
> there's no warning about text-based parsing nor a suggestion to use
> XML that I can see -- perhaps should be added?
>
> Dave

We should probably add something specifically for BLAST, yes.  Other  
text parsers should be fine.

Personally, I use XML or tabular output parsing simply b/c they are  
faster and do what I need.  I think we'll need to retain the  
capability for text-based BLAST parsing, but it will become extremely  
bloated long-term if we plan on continuing support for parsing all  
versions and flavors of BLAST, particularly if NCBI continues to  
change the output.

chris


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