A better breakdown...
fasta_file = sys.argv[1] # should be *.fa
> print 'loading dna from', fasta_file
> chroms = {}
> dna = None
> for l in open(fasta_file):
> if l.startswith('>'): # new chromosome
> if dna is not None:
> chroms[chrom] = dna
> chrom = l.strip().replace('>', '')
> dna = ''
> else:
> dna += l.rstrip()
> if dna is not None:
> chroms[chrom] = dna
>
CPython takes about 1.5 seconds to get to this point in the code, while pypy
hasn't passed this point in 30 minutes.
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