[Biococoa-dev] reading large fasta files

Koen van der Drift kvddrift at earthlink.net
Sun Oct 21 09:13:31 EDT 2007


I was trying to load a large fasta file (2 MB) in the Translation  
demo, and right now it takes a long time. Scott recently added  
BCCachedFastaFile for exactly this purpose, but the code in  
BCSequenceReader doesn't use it yet. How could we implement this in  
BCSequenceReader? One possibility is to always use BCCachedFastaFile  
for any fasta file. Or should we set a datasize limit in  
readFastaFile that determines when to use BCCachedFastaFile or the  
regular code? In the latter case, what would be a reasonable value  
for this?  For now I will implement to always use BCCachedFastaFile,  
but this can be change later, I will not delete any code ;-)


- Koen.

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