[Biococoa-dev] reading large fasta files
Koen van der Drift
kvddrift at earthlink.net
Sun Oct 21 09:13:31 EDT 2007
Hi,
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 ;-)
cheers,
- Koen.
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