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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