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

Chris Fields cjfields at uiuc.edu
Thu Mar 1 10:24:03 EST 2007


I do have a rough outline of what I think could be done:

http://www.bioperl.org/wiki/Handler-based_SeqIO_parsers

where you could switch out handlers to deal with incoming data  
chunks.  Any suggestions there are welcome.

I'll probably commit examples of the above in the next week or two  
(GenBank, EMBL, Swiss parsers using the same handlers) which don't  
use FTHelper.  So far I have all three passing tests based on genbank/ 
embl/swiss.t but they need a few more tweaks before I commit.

chris

On Mar 1, 2007, at 5:02 AM, Heikki Lehvaslaiho wrote:

> Chris,
>
> It was meant to collect code that was common to all three main  
> databases using
> similar feature tables.
>
> Now might be the time to optimise the parsing speed by removing it.  
> Do you
> have a plan how to do it?
>
> 	-Heikki
>
> On Tuesday 27 February 2007 22:57:40 Chris Fields wrote:
>> Could anyone tell me what FTHelper is used for?  From what I gather
>> it rolls up seqfeature data into a lightweight object but then
>> creates a SeqFeature::Generic anyway (at least for GenBank/EMBL/
>> Swiss), which seems to be a waste of memory and time.  Is there
>> something I'm missing (besides my sanity of course)?
>>
>> chris
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
> -- 
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>      _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
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>   _/  _/  _/  University of Western Cape, South Africa
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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