Algo attempt

best-codon.go

@@ -0,0 +1,105 @@
+package main
+
+import (
+    "encoding/csv"
+    "fmt"
+    "log"
+    "os"
+    "sort"
+    "strings"
+)
+
+// modified from https://stackoverflow.com/questions/37562873/most-idiomatic-way-to-select-elements-from-an-array-in-golang
+func filter(ss [][]string, test func([]string) bool) (ret [][]string) {
+    for _, s := range ss {
+        if test(s) {
+            ret = append(ret, s)
+        }
+    }
+    return
+}
+
+// from https://stackoverflow.com/questions/24999079/reading-csv-file-in-go
+func readCsvFile(filePath string) [][]string {
+    f, err := os.Open(filePath)
+    if err != nil {
+        log.Fatal("Unable to read input file " + filePath, err)
+    }
+    defer f.Close()
+
+    csvReader := csv.NewReader(f)
+    records, err := csvReader.ReadAll()
+    if err != nil {
+        log.Fatal("Unable to parse file as CSV for " + filePath, err)
+    }
+
+    return records
+}
+
+// from https://gobyexample.com/sorting-by-functions
+type byBestSynonym [][]string
+
+func (s byBestSynonym) Len() int {
+    return len(s)
+}
+
+func (s byBestSynonym) Swap(i, j int) {
+    s[i][1], s[j][1] = s[j][1], s[i][1]
+}
+
+func score(codon string) int {
+  return strings.Count(codon, "C") + strings.Count(codon, "G")
+}
+
+// sort by highest occurance of C and G
+func (s byBestSynonym) Less(i, j int) bool {
+    return score(s[i][1]) > score(s[j][1])
+}
+
+func bestCodon(amino string, virus_codon string, codons [][]string) string {
+  synonym := func(s []string) bool { return s[0] == amino }
+  synonyms := filter(codons, synonym)
+  sort.Sort(byBestSynonym(synonyms))
+  winner := synonyms[0][1]
+  // Never change a winning team:
+  if score(winner) == score(virus_codon) {
+    return virus_codon
+  }
+  return winner
+}
+
+
+func main() {
+	// Read the codon/amino acid table
+	codons := readCsvFile("codon-table-grouped.csv")[1:]
+
+	c2s:= make(map[string]string)
+	for _, element := range codons {
+		c2s[element[1]]=element[0]
+	}
+
+	// read the codons
+	virvac := readCsvFile("side-by-side.csv")[1:]
+
+	matches := 0.0
+	for _, element := range virvac {
+		vir:=element[1]
+		vac:=element[2]
+		var our string
+		fmt.Printf("%s v %s, amino: %s == %s. ",
+			vir, vac,
+			c2s[vir], c2s[vac])
+
+		our = bestCodon(c2s[vir], vir, codons)
+
+		fmt.Printf(" ")
+		if(vac == our) {
+			fmt.Printf("Matched the vaccine!\n")
+			matches++
+		} else {
+			fmt.Printf("No match (%s)\n", our)
+		}
+	}
+	fmt.Printf("%.1f%%\n", 100.0*matches/float64(len(virvac)))
+
+}