()
| 24 | } |
| 25 | |
| 26 | func ExampleTranslationTable_UpdateWeights() { |
| 27 | gfpTranslation := "MASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK*" |
| 28 | |
| 29 | sequenceWithCustomWeights := "ATGGCGAGCAAGGGCGAAGAGCTTTTTACTGGAGTGGTACCCATCCTTGTGGAGCTGGATGGGGATGTTAATGGGCACAAGTTTTCTGTGTCCGGTGAGGGGGAGGGTGACGCGACCTATGGCAAACTAACGTTGAAGTTTATCTGCACCACCGGCAAGCTCCCTGTCCCTTGGCCGACGCTGGTAACCACTTTTTCATACGGAGTGCAATGCTTTTCACGATACCCAGACCACATGAAACGGCACGACTTCTTCAAGAGCGCGATGCCAGAAGGTTATGTGCAAGAGCGTACGATCTCATTCAAGGACGACGGGAATTATAAGACAAGAGCAGAGGTGAAATTTGAGGGGGACACGTTAGTAAATCGGATTGAATTAAAGGGAATCGACTTTAAGGAGGATGGGAACATACTTGGTCACAAACTGGAATATAATTACAATTCACACAATGTTTACATCACTGCCGACAAGCAAAAAAATGGGATTAAAGCAAATTTCAAAATTCGGCATAATATTGAGGATGGTAGTGTCCAGCTCGCGGATCACTATCAGCAAAACACACCTATCGGAGACGGACCCGTTTTACTACCGGATAATCATTACTTAAGCACCCAATCAGCGTTATCCAAAGATCCGAACGAAAAACGTGACCACATGGTTCTCTTGGAGTTCGTCACCGCAGCTGGAATAACTCATGGAATGGACGAACTATACAAATAA" |
| 30 | |
| 31 | table, err := codon.NewTranslationTable(11) |
| 32 | if err != nil { |
| 33 | fmt.Printf("error running example: %s\n", err) |
| 34 | return |
| 35 | } |
| 36 | |
| 37 | // this example is using custom weights for different codons for Arginine. Use this if you would rather use your own |
| 38 | // codon weights, they can also be computed for you with `UpdateWeightsWithSequence`. |
| 39 | |
| 40 | err = table.UpdateWeights([]codon.AminoAcid{ |
| 41 | { |
| 42 | Letter: "R", |
| 43 | Codons: []codon.Codon{ |
| 44 | { |
| 45 | Triplet: "CGU", |
| 46 | Weight: 1, |
| 47 | }, |
| 48 | { |
| 49 | Triplet: "CGA", |
| 50 | Weight: 2, |
| 51 | }, |
| 52 | { |
| 53 | Triplet: "CGG", |
| 54 | Weight: 4, |
| 55 | }, |
| 56 | { |
| 57 | Triplet: "AGA", |
| 58 | Weight: 6, |
| 59 | }, |
| 60 | { |
| 61 | Triplet: "AGG", |
| 62 | Weight: 2, |
| 63 | }, |
| 64 | }, |
| 65 | }, |
| 66 | }) |
| 67 | if err != nil { |
| 68 | fmt.Println("Could not update weights in example") |
| 69 | } |
| 70 | |
| 71 | optimizedSequence, err := table.Optimize(gfpTranslation, 1) |
| 72 | if err != nil { |
| 73 | fmt.Printf("error running example: %s\n", err) |
| 74 | return |
| 75 | } |
| 76 | |
| 77 | fmt.Println(optimizedSequence == sequenceWithCustomWeights) |
| 78 | // output: true |
| 79 | } |
| 80 | |
| 81 | func ExampleTranslationTable_Optimize() { |
| 82 | gfpTranslation := "MASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK*" |
nothing calls this directly
no test coverage detected