[Bioperl-l] results problem with StandAloneBlast

Sendu Bala sb at mrc-dunn.cam.ac.uk
Mon Jun 5 05:57:52 EDT 2006

Chris Fields wrote:
> On Jun 4, 2006, at 9:08 AM, Jason Stajich wrote:
>> If you want to rewind the parser then (assuming you are using a 
>> filestream and not a data stream from the web or zcat or something) 
>> just reset the filehandle
>> seek($searchio->_fh, 0);
>> but then you'll have to re-parse everything and pay that cost twice - 
>> it makes more sense to me to just save the results and put them in 
>> list if you are going to deliberately make two passes over all the 
>> results.    You either pay the cost of memory (keeping all the 
>> objects) or time (reparse the results).
> I agree there isn't any really good reason to rewind the parser; I was 
> mainly just curious how this was accomlished.

Didn't you already explain why seeking a SearchIO wouldn't work? And 
indeed, didn't Genevieve already try to do this after I suggested it and 
  found that it didn't work?


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