Yes, Vincent's way is the better way to go. To elaborate more on the
problem, string appending is O(N^2) while appending to a list and then
joining is an O(N) operation. Why CPython is faster than Pypy at doing
the less efficient way is something that I'm not fully sure about, but
I believe that it might have to do with the differing memory
management strategies.
On Thu, Aug 18, 2011 at 4:24 PM, Vincent Legoll
<vincent.leg...@gmail.com> wrote:
> Hello,
>
> Try this:
>
> import sys
>
> fasta_file = sys.argv[1] # should be *.fa
> print 'loading dna from', fasta_file
> chroms = {}
> dna = []
> for l in open(fasta_file):
> if l.startswith('>'): # new chromosome
> if len(dna) > 0:
> chroms[chrom] = ''.join(dna)
> chrom = l.strip().replace('>', '')
> dna = []
> else:
> dna.append(l.rstrip())
> if len(dna) > 0:
> chroms[chrom] = ''.join(dna)
>
> --
> Vincent Legoll
> _______________________________________________
> pypy-dev mailing list
> pypy-dev@python.org
> http://mail.python.org/mailman/listinfo/pypy-dev
>
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