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| dna = """ACAAGATGCCATTGTCCCCCGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCACCGCTGCCCTGCC | |
| CCTGGAGGGTGGCCCCACCGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGGAATAAGGAAAAGCAGC | |
| CTCCTGACTTTCCTCGCTTGGTGGTTTGAGTGGACCTCCCAGGCCAGTGCCGGGCCCCTCATAGGAGAGG | |
| AAGCTCGGGAGGTGGCCAGGCGGCAGGAAGGCGCACCCCCCCAGCAATCCGCGCGCCGGGACAGAATGCC | |
| CTGCAGGAACTTCTTCTGGAAGACCTTCTCCTCCTGCAAATAAAACCTCACCCATGAATGCTCACGCAAG | |
| TTTAATTACAGACCTGAAG""".replace("\n", "").replace("\t", "").replace("\r", "").replace(" ", "") | |
| #1 using regular expression | |
| import re | |
| print re.split("TAG|TAA|TGA", dna) | |
| #2 using only split | |
| split_on_tag = [] | |
| split_on_taa = [] | |
| split_on_tga = [] | |
| for fragment in dna.split("TAG"): | |
| split_on_tag.append(fragment) | |
| for fragment in split_on_tag: | |
| split_on_taa += fragment.split("TAA") | |
| for fragment in split_on_taa: | |
| split_on_tga += fragment.split("TGA") | |
| print split_on_tga | |
| #3 | |
| haku = dna.replace("TAG", " ").replace("TAA", " ").replace("TGA", " ").split(" ") | |
| print haku | |
| #4 using low level loops | |
| stop_codons = {"TAG", "TAA", "TGA"} | |
| fragments = [] | |
| i = 0 | |
| begin = 0 | |
| while (i < len(dna)): | |
| if dna[i:i+3] in stop_codons: | |
| fragments.append(dna[begin:i]) | |
| begin = i + 3 | |
| i += 3 | |
| else: | |
| i += 1 | |
| if (begin < len(dna)): | |
| fragments.append(dna[begin:]) | |
| print fragments |
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