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Fixing updateweights example (#435)
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* generate codon table in constructor rather than at buildtime

* update tests to handle constructor error, since tables are no longer generated at buildtime

* update examples to handle constructor error, since tables are no longer generated at buildtime

* write a proper deepcopy func + test
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@cachemoi
cachemoi authored Jan 5, 2024
1 parent efd4540 commit 43c015b
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Showing 3 changed files with 325 additions and 90 deletions.
126 changes: 80 additions & 46 deletions synthesis/codon/codon.go
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Original file line number Diff line number Diff line change
Expand Up @@ -117,19 +117,46 @@ type TranslationTable struct {
}

// Copy returns a deep copy of the translation table. This is to prevent an unintended update of data used in another
// process, since the tables are generated at build time.
func (table *TranslationTable) Copy() *TranslationTable {
return &TranslationTable{
StartCodons: table.StartCodons,
StopCodons: table.StopCodons,
AminoAcids: table.AminoAcids,
// process.
func (table *TranslationTable) Copy() (*TranslationTable, error) {
newTranslationMap := map[string]string{}
newStartCodonTable := map[string]string{}

StartCodonTable: table.StartCodonTable,
TranslationMap: table.TranslationMap,
Choosers: table.Choosers,
for k, v := range table.TranslationMap {
newTranslationMap[k] = v
}

Stats: table.Stats,
for k, v := range table.StartCodonTable {
newStartCodonTable[k] = v
}

newAAs := []AminoAcid{}
for _, v := range table.AminoAcids {
newAAs = append(newAAs, AminoAcid{
Letter: "",
Codons: append([]Codon{}, v.Codons...),
})
}

newChoosers, err := newAminoAcidChoosers(newAAs)
if err != nil {
return nil, err
}

return &TranslationTable{
StartCodons: append([]string{}, table.StartCodons...),
StopCodons: append([]string{}, table.StopCodons...),
AminoAcids: append([]AminoAcid{}, table.AminoAcids...),

TranslationMap: newTranslationMap,
StartCodonTable: newStartCodonTable,
Choosers: newChoosers,

Stats: &Stats{
StartCodonCount: table.Stats.StartCodonCount,
GeneCount: table.Stats.GeneCount,
},
}, nil
}

// GetWeightedAminoAcids returns the amino acids along with their associated codon weights
Expand Down Expand Up @@ -385,7 +412,7 @@ Tim
******************************************************************************/

// Function to generate default codon tables from NCBI https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
func generateCodonTable(aminoAcids, starts string) *TranslationTable {
func generateCodonTable(aminoAcids, starts string) (*TranslationTable, error) {
base1 := "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG"
base2 := "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG"
base3 := "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG"
Expand Down Expand Up @@ -432,7 +459,7 @@ func generateCodonTable(aminoAcids, starts string) *TranslationTable {
// This function is run at buildtime and failure here means we have an invalid codon table.
chooser, err := newAminoAcidChoosers(aminoAcidSlice)
if err != nil {
panic(fmt.Errorf("tried to generate an invalid codon table %w", err))
return nil, fmt.Errorf("tried to generate an invalid codon table %w", err)
}

return &TranslationTable{
Expand All @@ -443,41 +470,42 @@ func generateCodonTable(aminoAcids, starts string) *TranslationTable {
StartCodonTable: startCodonsMap,
Choosers: chooser,
Stats: NewStats(),
}
}, nil
}

// NewTranslationTable takes the index of desired NCBI codon table and returns it.
func NewTranslationTable(index int) *TranslationTable {
return translationTablesByNumber[index].Copy()
func NewTranslationTable(index int) (*TranslationTable, error) {
return generateCodonTable(translationTablesByNumber[index][0], translationTablesByNumber[index][1])
}

// translationTablesByNumber stores all codon tables published by NCBI https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi using numbered indices.
var translationTablesByNumber = map[int]*TranslationTable{
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------------")}
// translationTablesByNumber stores all data necessary to generate codon tables from sequences published by NCBI https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi using numbered indices.
var translationTablesByNumber = map[int][]string{
1: {"FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "---M------**--*----M---------------M----------------------------"},
2: {"FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG", "----------**--------------------MMMM----------**---M------------"},
3: {"FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------**----------------------MM---------------M------------"},
4: {"FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--MM------**-------M------------MMMM---------------M------------"},
5: {"FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG", "---M------**--------------------MMMM---------------M------------"},
6: {"FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--------------*--------------------M----------------------------"},
9: {"FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG", "----------**-----------------------M---------------M------------"},
10: {"FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------**-----------------------M----------------------------"},
11: {"FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "---M------**--*----M------------MMMM---------------M------------"},
12: {"FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------**--*----M---------------M----------------------------"},
13: {"FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG", "---M------**----------------------MM---------------M------------"},
14: {"FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG", "-----------*-----------------------M----------------------------"},
16: {"FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------*---*--------------------M----------------------------"},
21: {"FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG", "----------**-----------------------M---------------M------------"},
22: {"FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "------*---*---*--------------------M----------------------------"},
23: {"FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--*-------**--*-----------------M--M---------------M------------"},
24: {"FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG", "---M------**-------M---------------M---------------M------------"},
25: {"FFLLSSSSYY**CCGWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "---M------**-----------------------M---------------M------------"},
26: {"FFLLSSSSYY**CC*WLLLAPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------**--*----M---------------M----------------------------"},
27: {"FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--------------*--------------------M----------------------------"},
28: {"FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------**--*--------------------M----------------------------"},
29: {"FFLLSSSSYYYYCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--------------*--------------------M----------------------------"},
30: {"FFLLSSSSYYEECC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--------------*--------------------M----------------------------"},
31: {"FFLLSSSSYYEECCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------**-----------------------M----------------------------"},
33: {"FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG", "---M-------*-------M---------------M---------------M------------"},
}

/******************************************************************************
Nov, 20, 2020
Expand Down Expand Up @@ -591,7 +619,10 @@ func CompromiseCodonTable(firstCodonTable, secondCodonTable *TranslationTable, c
//
// this take start and stop strings from first table
// and use them as start + stops in final codonTable
mergedTable := firstCodonTable.Copy()
mergedTable, err := firstCodonTable.Copy()
if err != nil {
return nil, err
}

// Check if cutOff is too high or low (this is converted to a percent)
if cutOff < 0 {
Expand Down Expand Up @@ -662,7 +693,7 @@ func CompromiseCodonTable(firstCodonTable, secondCodonTable *TranslationTable, c
finalAminoAcids = append(finalAminoAcids, AminoAcid{firstAa.Letter, finalCodons})
}

err := mergedTable.UpdateWeights(finalAminoAcids)
err = mergedTable.UpdateWeights(finalAminoAcids)
if err != nil {
return nil, err
}
Expand All @@ -689,9 +720,12 @@ func AddCodonTable(firstCodonTable, secondCodonTable *TranslationTable) (*Transl
finalAminoAcids = append(finalAminoAcids, AminoAcid{firstAa.Letter, finalCodons})
}

mergedTable := firstCodonTable.Copy()
mergedTable, err := firstCodonTable.Copy()
if err != nil {
return nil, err
}

err := mergedTable.UpdateWeights(finalAminoAcids)
err = mergedTable.UpdateWeights(finalAminoAcids)
if err != nil {
return nil, err
}
Expand Down
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