patched genbank parser and builder to handle BASE COUNT. (#386)

bebop · Oct 12, 2023 · 2d5d8c4 · 2d5d8c4
1 parent f2310db
commit 2d5d8c4
Show file tree

Hide file tree

Showing 2 changed files with 33 additions and 1 deletion.
diff --git a/data/sample.gbk b/data/sample.gbk
@@ -77,6 +77,7 @@ FEATURES             Location/Qualifiers
                      KDDQIITETEVFDEFRSSLNSLIMHLEKLPKVNDDTITFEAVINAIELELGHKLDRNR
                      RVDSLEEKAEIERDSNWVKCQEDENLPDNNGFQPPKIKLTSLVGSDVGPLIIHQFSEK
                      LISGDDKILNGVYSQYEEGESIFGSLF"
+BASE COUNT    67070277 a   48055043 c   48111528 g   67244164 t   18475410 n                    
 ORIGIN
         1 gatcctccat atacaacggt atctccacct caggtttaga tctcaacaac ggaaccattg
        61 ccgacatgag acagttaggt atcgtcgaga gttacaagct aaaacgagca gtagtcagct

diff --git a/io/genbank/genbank.go b/io/genbank/genbank.go
@@ -57,6 +57,7 @@ type Meta struct {
 	Origin               string            `json:"origin"`
 	Locus                Locus             `json:"locus"`
 	References           []Reference       `json:"references"`
+	BaseCount            []BaseCount       `json:"base_count"`
 	Other                map[string]string `json:"other"`
 	Name                 string            `json:"name"`
 	SequenceHash         string            `json:"sequence_hash"`
@@ -109,6 +110,12 @@ type Location struct {
 	SubLocations      []Location `json:"sub_locations"`
 }
 
+// BaseCount is a struct that holds the base counts for a sequence.
+type BaseCount struct {
+	Base  string
+	Count int
+}
+
 // Precompiled regular expressions:
 var (
 	basePairRegex         = regexp.MustCompile(` \d* \w{2} `)
@@ -315,6 +322,13 @@ func BuildMulti(sequences []Genbank) ([]byte, error) {
 			gbkString.WriteString(BuildFeatureString(feature))
 		}
 
+		if len(sequence.Meta.BaseCount) > 0 {
+			gbkString.WriteString("BASE COUNT    ")
+			for _, baseCount := range sequence.Meta.BaseCount {
+				gbkString.WriteString(strconv.Itoa(baseCount.Count) + " " + baseCount.Base + "   ")
+			}
+			gbkString.WriteString("\n")
+		}
 		// start writing sequence section.
 		gbkString.WriteString("ORIGIN\n")
 
@@ -378,7 +392,7 @@ type parseLoopParameters struct {
 	emptyAttribute   bool
 	sequenceBuilder  strings.Builder
 	parseStep        string
-	genbank          Genbank // since we are scanning lines we need a Genbank struct to store the data outside the loop.// since we are scanning lines we need a Genbank struct to store the data outside the loop.
+	genbank          Genbank // since we are scanning lines we need a Genbank struct to store the data outside the loop.
 	feature          Feature
 	features         []Feature
 	metadataTag      string
@@ -484,6 +498,23 @@ func ParseMultiNth(r io.Reader, count int) ([]Genbank, error) {
 			}
 		case "features":
 
+			baseCountFlag := strings.Contains(line, "BASE COUNT") // example string for BASE COUNT: "BASE COUNT    67070277 a   48055043 c   48111528 g   67244164 t   18475410 n"
+			if baseCountFlag {
+				fields := strings.Fields(line)
+				for countIndex := 2; countIndex < len(fields)-1; countIndex += 2 { // starts at two because we don't want to include "BASE COUNT" in our fields
+					count, err := strconv.Atoi(fields[countIndex])
+					if err != nil {
+						return []Genbank{}, err
+					}
+
+					baseCount := BaseCount{
+						Base:  fields[countIndex+1],
+						Count: count,
+					}
+					parameters.genbank.Meta.BaseCount = append(parameters.genbank.Meta.BaseCount, baseCount)
+				}
+				break
+			}
 			// Switch to sequence parsing
 			originFlag := strings.Contains(line, "ORIGIN") // we detect the beginning of the sequence with "ORIGIN"
 			if originFlag {