On Wed, Apr 10, 2013 at 8:32 AM, Danny Yoo <[email protected]> wrote:
> Hi Ali, > > Again, I recommend not reinventing a FASTA parser unless you really > need something custom here. In this particular case, the function > ReadFasta here is slow on large inputs. The culprit is the set of > lines: > > if line[0]=='>': > prevLine=line[1:] > dictFasta[prevLine]='' > else: > Sure, I myself use biopythin as well, but just wanted to mention that it's not a big hassle, in particular if you need to load it just once. You have a very legitimate point about the order of execution of my suggested code. Ali
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