Add optimization and translation functions for sequences #11
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,142 @@ | ||
| package main | ||
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| import ( | ||
| "math/rand" | ||
| "time" | ||
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| weightedRand "github.com/mroth/weightedrand" | ||
| ) | ||
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| // Codon holds information for a codon triplet in a struct | ||
| type Codon struct { | ||
| Triplet string | ||
| Occurrence int | ||
| } | ||
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| // AminoAcid holds information for an amino acid and related codons in a struct in a struct | ||
| type AminoAcid struct { | ||
| Letter string | ||
| Codons []Codon | ||
| } | ||
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| // CodonTable holds information for a codon table. | ||
| type CodonTable struct { | ||
| StartCodons []string | ||
| StopCodons []string | ||
| AminoAcids []AminoAcid | ||
| } | ||
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| // Generate map of amino acid -> codon chooser | ||
| func (codonTable CodonTable) generateOptimizationTable() map[string]weightedRand.Chooser { | ||
| rand.Seed(time.Now().UTC().UnixNano()) | ||
| var optimizationMap = make(map[string]weightedRand.Chooser) | ||
| for _, aminoAcid := range codonTable.AminoAcids { | ||
| // Get list of triplets and their weights | ||
| codonChoices := make([]weightedRand.Choice, len(aminoAcid.Codons)) | ||
| totals := 0 | ||
| for _, codon := range aminoAcid.Codons { | ||
| codonChoices = append(codonChoices, weightedRand.Choice{Item: codon.Triplet, Weight: uint(codon.Occurrence)}) | ||
| totals += codon.Occurrence | ||
| } | ||
| optimizationMap[aminoAcid.Letter] = weightedRand.NewChooser(codonChoices...) | ||
| } | ||
| return optimizationMap | ||
| } | ||
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| // Optimize takes an amino acid sequence and CodonTable and returns an optimized codon sequence | ||
| func Optimize(aminoAcids string, codonTable CodonTable) string { | ||
| var codons string | ||
| optimizationTable := codonTable.generateOptimizationTable() | ||
| for _, aminoAcid := range aminoAcids { | ||
| codons += optimizationTable[string(aminoAcid)].Pick().(string) | ||
| } | ||
| return codons | ||
| } | ||
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| // Generate map of codons -> amino acid | ||
| func (codonTable CodonTable) generateTranslationTable() map[string]string { | ||
| var translationMap = make(map[string]string) | ||
| for _, aminoAcid := range codonTable.AminoAcids { | ||
| for _, codon := range aminoAcid.Codons { | ||
| translationMap[codon.Triplet] = aminoAcid.Letter | ||
| } | ||
| } | ||
| return translationMap | ||
| } | ||
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| // Translate translates a codon sequence to an amino acid sequence | ||
| func Translate(nucleotides string, codonTable CodonTable) string { | ||
| var aminoAcids string | ||
| translationTable := codonTable.generateTranslationTable() | ||
| length := len(nucleotides) / 3 // Assumes input sequences are divisible by 3 | ||
| for i := 0; length > i; i++ { | ||
| aminoAcids += translationTable[nucleotides[i*3:(i+1)*3]] | ||
| } | ||
| return aminoAcids | ||
| } | ||
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| // Function to generate default codon tables from NCBI https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi | ||
| func generateCodonTable(aas, starts string) CodonTable { | ||
|
There was a problem hiding this comment. What does aas stand for here? Amino acid string? There was a problem hiding this comment. It stands for amino acids. On the link, they just name it "AAs", so I just copied their nomenclature (also why starts is named starts) |
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| base1 := "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG" | ||
| base2 := "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG" | ||
| base3 := "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG" | ||
| // Add triplets to an amino acid -> triplet map, and if a possible start codon, add to start codon list | ||
| var aminoAcidMap = make(map[rune][]Codon) | ||
| var startCodons []string | ||
| var stopCodons []string | ||
| for i, aminoAcid := range aas { | ||
| if _, ok := aminoAcidMap[aminoAcid]; ok == false { | ||
| aminoAcidMap[aminoAcid] = []Codon{} | ||
| } | ||
| triplet := string([]byte{base1[i], base2[i], base3[i]}) | ||
| aminoAcidMap[aminoAcid] = append(aminoAcidMap[aminoAcid], Codon{triplet, 0}) | ||
| if starts[i] == 77 { // M rune | ||
| startCodons = append(startCodons, triplet) | ||
| } | ||
| if starts[i] == 42 { // * rune | ||
| stopCodons = append(stopCodons, triplet) | ||
| } | ||
| } | ||
| // Convert amino acid -> triplet map to an amino acid list | ||
| var aminoAcidSlice []AminoAcid | ||
| for k, v := range aminoAcidMap { | ||
| aminoAcidSlice = append(aminoAcidSlice, AminoAcid{string(k), v}) | ||
| } | ||
| return CodonTable{startCodons, stopCodons, aminoAcidSlice} | ||
| } | ||
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| // DefaultCodonTables stores all codon tables published by NCBI https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi | ||
| var DefaultCodonTables = map[int]CodonTable{ | ||
| 1: generateCodonTable("FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "---M------**--*----M---------------M----------------------------"), | ||
| 2: generateCodonTable("FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG", "----------**--------------------MMMM----------**---M------------"), | ||
| 3: generateCodonTable("FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------**----------------------MM---------------M------------"), | ||
| 4: generateCodonTable("FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--MM------**-------M------------MMMM---------------M------------"), | ||
| 5: generateCodonTable("FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG", "---M------**--------------------MMMM---------------M------------"), | ||
| 6: generateCodonTable("FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--------------*--------------------M----------------------------"), | ||
| 9: generateCodonTable("FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG", "----------**-----------------------M---------------M------------"), | ||
| 10: generateCodonTable("FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------**-----------------------M----------------------------"), | ||
| 11: generateCodonTable("FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "---M------**--*----M------------MMMM---------------M------------"), | ||
| 12: generateCodonTable("FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------**--*----M---------------M----------------------------"), | ||
| 13: generateCodonTable("FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG", "---M------**----------------------MM---------------M------------"), | ||
| 14: generateCodonTable("FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG", "-----------*-----------------------M----------------------------"), | ||
| 16: generateCodonTable("FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------*---*--------------------M----------------------------"), | ||
| 21: generateCodonTable("FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG", "----------**-----------------------M---------------M------------"), | ||
| 22: generateCodonTable("FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "------*---*---*--------------------M----------------------------"), | ||
| 23: generateCodonTable("FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--*-------**--*-----------------M--M---------------M------------"), | ||
| 24: generateCodonTable("FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG", "---M------**-------M---------------M---------------M------------"), | ||
| 25: generateCodonTable("FFLLSSSSYY**CCGWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "---M------**-----------------------M---------------M------------"), | ||
| 26: generateCodonTable("FFLLSSSSYY**CC*WLLLAPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------**--*----M---------------M----------------------------"), | ||
| 27: generateCodonTable("FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--------------*--------------------M----------------------------"), | ||
| 28: generateCodonTable("FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------**--*--------------------M----------------------------"), | ||
| 29: generateCodonTable("FFLLSSSSYYYYCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--------------*--------------------M----------------------------"), | ||
| 30: generateCodonTable("FFLLSSSSYYEECC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--------------*--------------------M----------------------------"), | ||
| 31: generateCodonTable("FFLLSSSSYYEECCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------**-----------------------M----------------------------"), | ||
| 33: generateCodonTable("FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG", "---M-------*-------M---------------M---------------M------------")} | ||
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| //func main() { | ||
| // rand.Seed(time.Now().UTC().UnixNano()) | ||
| // codonTable := CodonTable{[]string{},[]string{},[]aminoAcid{{"M",[]Codon{{"ATG", 1}}},{"G",[]Codon{{"GGA", 1}}},{"*",[]Codon{{"TAA",1},{"TGA",1}}}}} | ||
| // translation := Translate("ATGGGCTGA", DefaultCodonTables[1]) | ||
|
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| // fmt.Println(optimize(translation,codonTable)) | ||
| //} | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| package main | ||
|
|
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| import ( | ||
| "testing" | ||
| ) | ||
|
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| func TestTranslation(t *testing.T) { | ||
| gfpTranslation := "MASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK*" | ||
| gfpDnaSequence := "ATGGCTAGCAAAGGAGAAGAACTTTTCACTGGAGTTGTCCCAATTCTTGTTGAATTAGATGGTGATGTTAATGGGCACAAATTTTCTGTCAGTGGAGAGGGTGAAGGTGATGCTACATACGGAAAGCTTACCCTTAAATTTATTTGCACTACTGGAAAACTACCTGTTCCATGGCCAACACTTGTCACTACTTTCTCTTATGGTGTTCAATGCTTTTCCCGTTATCCGGATCATATGAAACGGCATGACTTTTTCAAGAGTGCCATGCCCGAAGGTTATGTACAGGAACGCACTATATCTTTCAAAGATGACGGGAACTACAAGACGCGTGCTGAAGTCAAGTTTGAAGGTGATACCCTTGTTAATCGTATCGAGTTAAAAGGTATTGATTTTAAAGAAGATGGAAACATTCTCGGACACAAACTCGAGTACAACTATAACTCACACAATGTATACATCACGGCAGACAAACAAAAGAATGGAATCAAAGCTAACTTCAAAATTCGCCACAACATTGAAGATGGATCCGTTCAACTAGCAGACCATTATCAACAAAATACTCCAATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTACCTGTCGACACAATCTGCCCTTTCGAAAGATCCCAACGAAAAGCGTGACCACATGGTCCTTCTTGAGTTTGTAACTGCTGCTGGGATTACACATGGCATGGATGAGCTCTACAAATAA" | ||
| if got := Translate(gfpDnaSequence,DefaultCodonTables[11]); got != gfpTranslation { | ||
| t.Errorf("TestTranslation has failed. Translate has returned %q, want %q", got, gfpTranslation) | ||
| } | ||
| } |
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Maybe I don't know go very well. But is this a
for loopin afor loopin amap>.>