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- In [75]: from Bio.Seq import Seq
- ...:
- ...: def my_reverse_complement(seq):
- ...: return Seq(seq).reverse_complement()
- ...:
- In [76]: import string
- ...: tab = str.maketrans("ACTG", "TGAC")
- ...:
- ...: def reverse_complement_table(seq):
- ...: return seq.translate(tab)[::-1]
- ...:
- In [77]: s = 'ATGCGTA'* 100000
- In [78]: %timeit my_reverse_complement(s)
- 100 loops, best of 3: 1.63 ms per loop
- In [79]: %timeit reverse_complement_table(s)
- 1000 loops, best of 3: 1.33 ms per loop
- In [80]: %timeit my_reverse_complement(s)
- 1000 loops, best of 3: 1.54 ms per loop
- In [81]: %timeit reverse_complement_table(s)
- 1000 loops, best of 3: 1.29 ms per loop
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