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:
dictFasta[prevLine]=dictFasta[prevLine]+line
which looks innocent on its own, but it is an O(n^2) string-appending
algorithm if we walk across a very long sequence such as a
chromosome. The folks who have written the Biopython FASTA parser have
almost certainly already considered this pitfall.
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