created parser regression test for nested sublocations. (#385)

* created parser regression test for nested sublocations. * integrating @abondrn's fix to genbank parser. * fixed lint issues. * added data for regression test. Co-authored-by: Alex <[email protected]> Co-authored-by: Alex <[email protected]>
bebop · Oct 11, 2023 · f2310db · f2310db
1 parent 5bd6a5d
commit f2310db
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Showing 3 changed files with 50 additions and 14 deletions.
diff --git a/data/parseLocationRegressionTest.json b/data/parseLocationRegressionTest.json
@@ -0,0 +1 @@
+{"start":0,"end":0,"complement":false,"join":true,"five_prime_partial":false,"three_prime_partial":false,"gbk_location_string":"join(complement(5306942..5307394),complement(5304401..5305029),complement(5303328..5303393),complement(5301928..5302004))","sub_locations":[{"start":5306941,"end":5307394,"complement":true,"join":false,"five_prime_partial":false,"three_prime_partial":false,"gbk_location_string":"join(complement(5306942..5307394),complement(5304401..5305029),complement(5303328..5303393),complement(5301928..5302004))","sub_locations":null},{"start":5304400,"end":5305029,"complement":true,"join":false,"five_prime_partial":false,"three_prime_partial":false,"gbk_location_string":"join(complement(5306942..5307394),complement(5304401..5305029),complement(5303328..5303393),complement(5301928..5302004))","sub_locations":null},{"start":5303327,"end":5303393,"complement":true,"join":false,"five_prime_partial":false,"three_prime_partial":false,"gbk_location_string":"join(complement(5306942..5307394),complement(5304401..5305029),complement(5303328..5303393),complement(5301928..5302004))","sub_locations":null},{"start":5301927,"end":5302004,"complement":true,"join":false,"five_prime_partial":false,"three_prime_partial":false,"gbk_location_string":"join(complement(5306942..5307394),complement(5304401..5305029),complement(5303328..5303393),complement(5301928..5302004))","sub_locations":null}]}
diff --git a/io/genbank/genbank.go b/io/genbank/genbank.go
@@ -811,8 +811,8 @@ func getSourceOrganism(metadataData []string) (string, string, []string) {
 func parseLocation(locationString string) (Location, error) {
 	var location Location
 	location.GbkLocationString = locationString
-	if !(strings.ContainsAny(locationString, "(")) { // Case checks for simple expression of x..x
-		if !(strings.ContainsAny(locationString, ".")) { //Case checks for simple expression x
+	if !strings.ContainsAny(locationString, "(") { // Case checks for simple expression of x..x
+		if !strings.ContainsAny(locationString, ".") { //Case checks for simple expression x
 			position, err := strconv.Atoi(locationString)
 			if err != nil {
 				return Location{}, err
@@ -841,26 +841,34 @@ func parseLocation(locationString string) (Location, error) {
 			if strings.ContainsAny(expression, "(") {
 				firstInnerParentheses := strings.Index(expression, "(")
 				ParenthesesCount := 1
-				comma := 0
-				for i := 1; ParenthesesCount > 0; i++ { // "(" is at 0, so we start at 1
-					comma = i
-					switch expression[firstInnerParentheses+i] {
-					case []byte("(")[0]:
+				prevSubLocationStart := 0
+				for i := firstInnerParentheses + 1; i < len(expression); i++ { // "(" is at 0, so we start at 1
+					switch expression[i] {
+					case '(':
 						ParenthesesCount++
-					case []byte(")")[0]:
+					case ')':
 						ParenthesesCount--
+					case ',':
+						if ParenthesesCount == 0 {
+							parsedSubLocation, err := parseLocation(expression[prevSubLocationStart:i])
+							if err != nil {
+								return Location{}, err
+							}
+							parsedSubLocation.GbkLocationString = locationString
+							location.SubLocations = append(location.SubLocations, parsedSubLocation)
+							prevSubLocationStart = i + 1
+						}
 					}
 				}
-				parseLeftLocation, err := parseLocation(expression[:firstInnerParentheses+comma+1])
-				if err != nil {
-					return Location{}, err
+				if ParenthesesCount != 0 {
+					return Location{}, fmt.Errorf("Unbalanced parentheses")
 				}
-				parseRightLocation, err := parseLocation(expression[2+firstInnerParentheses+comma:])
+				parsedSubLocation, err := parseLocation(expression[prevSubLocationStart:])
 				if err != nil {
 					return Location{}, err
 				}
-
-				location.SubLocations = append(location.SubLocations, parseLeftLocation, parseRightLocation)
+				parsedSubLocation.GbkLocationString = locationString
+				location.SubLocations = append(location.SubLocations, parsedSubLocation)
 			} else { // This is the default join(x..x,x..x)
 				for _, numberRange := range strings.Split(expression, ",") {
 					joinLocation, err := parseLocation(numberRange)

diff --git a/io/genbank/genbank_test.go b/io/genbank/genbank_test.go
@@ -1,7 +1,9 @@
 package genbank
 
 import (
+	"encoding/json"
 	"errors"
+	"fmt"
 	"io"
 	"os"
 	"path/filepath"
@@ -160,6 +162,31 @@ func TestPartialLocationParseRegression(t *testing.T) {
 	}
 }
 
+func TestSubLocationStringParseRegression(t *testing.T) {
+	location := "join(complement(5306942..5307394),complement(5304401..5305029),complement(5303328..5303393),complement(5301928..5302004))"
+	parsedLocation, err := parseLocation(location)
+	if err != nil {
+		t.Errorf("Failed to parse location string. Got err: %s", err)
+	}
+	jsonFile, err := os.Open("../../data/parseLocationRegressionTest.json")
+	// if we os.Open returns an error then handle it
+	if err != nil {
+		fmt.Println(err)
+	}
+	defer jsonFile.Close()
+
+	byteValue, _ := io.ReadAll(jsonFile)
+	var testParsedLocation Location
+	err = json.Unmarshal(byteValue, &testParsedLocation)
+	if err != nil {
+		t.Errorf("Failed to unmarshal json. Got err: %s", err)
+	}
+
+	if diff := cmp.Diff(parsedLocation, testParsedLocation); diff != "" {
+		t.Errorf("Failed to parse sublocation string. Got this diff:\n%s", diff)
+	}
+}
+
 func TestSnapgeneGenbankRegression(t *testing.T) {
 	snapgene, err := Read("../../data/puc19_snapgene.gb")