Rename primer features to primer_bind on export

TeselaGen · Apr 8, 2021 · ebc286e · ebc286e
1 parent 683aa3a
commit ebc286e
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Showing 8 changed files with 45 additions and 29 deletions.
diff --git a/package.json b/package.json
@@ -50,7 +50,7 @@
     "nwb": "^0.23.0",
     "prettier": "^1.16.4",
     "ve-range-utils": "^2.5.9",
-    "ve-sequence-utils": "5.0.0"
+    "ve-sequence-utils": "5.1.0"
   },
   "peerDependencies": {
     "ve-range-utils": "*",

diff --git a/src/parsers/genbankToJson.js b/src/parsers/genbankToJson.js
@@ -216,18 +216,27 @@ function genbankToJson(string, options = {}) {
   );
   // default sequence json has primers at the top level separate from features, e.g. parsedSequence: { primers: [ {}, {} ], features: [ {}, {} ] }
   // if options.primersAsFeatures is set to true, primers are included in features with type set to primer
-  if (!options.primersAsFeatures) {
-    for (let i = 0; i < results.length; i++) {
-      if (results[i].success) {
-        results[i].parsedSequence.primers = results[
-          i
-        ].parsedSequence.features.filter((feat) => feat.type === "primer");
-        results[i].parsedSequence.features = results[
-          i
-        ].parsedSequence.features.filter((feat) => feat.type !== "primer");
+
+  results.forEach((result) => {
+    if (result.success) {
+      const sequence = result.parsedSequence;
+      sequence.features.forEach((feat) => {
+        if (feat.type === "primer") {
+          feat.type = "primer_bind";
+        }
+      });
+
+      if (!options.primersAsFeatures) {
+        sequence.primers = sequence.features.filter(
+          (feat) => feat.type === "primer_bind"
+        );
+        sequence.features = sequence.features.filter(
+          (feat) => feat.type !== "primer_bind"
+        );
       }
     }
-  }
+  });
+
   return results;
 
   function endSeq() {

diff --git a/src/parsers/utils/validateSequence.js b/src/parsers/utils/validateSequence.js
@@ -208,6 +208,13 @@ export default function validateSequence(sequence, options = {}) {
       feature.strand = 1;
     }
     let invalidFeatureType;
+    if (
+      feature.type &&
+      typeof feature.type === "string" &&
+      feature.type.toLowerCase() === "primer"
+    ) {
+      feature.type = "primer_bind";
+    }
     if (
       !feature.type ||
       typeof feature.type !== "string" ||

diff --git a/src/test/genbankToJson.test.js b/src/test/genbankToJson.test.js
@@ -410,7 +410,7 @@ ORIGIN
     });
   });
 
-  it("parses a gb with features of type primer, outputs json w/primers at top level by default", function() {
+  it("parses a gb with features of type primer_bind, outputs json w/primers at top level by default", function() {
     const string = fs.readFileSync(
       path.join(__dirname, "./testData/genbank/testing_primers.gb"),
       "utf8"
@@ -441,15 +441,15 @@ ORIGIN
     result[0].parsedSequence.primers.should.containSubset([
       {
         notes: {},
-        type: "primer",
+        type: "primer_bind",
         strand: 1,
         name: "primer1",
         start: 5,
         end: 9,
       },
       {
         notes: {},
-        type: "primer",
+        type: "primer_bind",
         strand: 1,
         name: "primer2",
         start: 17,
@@ -462,7 +462,7 @@ ORIGIN
     });
   });
 
-  it("parses a gb with features of type primer, outputs json w/primers as features of type primer because primersAsFeatures = true", function() {
+  it("parses a gb with features of type primer_bind, outputs json w/primers as features of type primer_bind because primersAsFeatures = true", function() {
     const string = fs.readFileSync(
       path.join(__dirname, "./testData/genbank/testing_primers.gb"),
       "utf8"
@@ -483,7 +483,7 @@ ORIGIN
       },
       {
         notes: {},
-        type: "primer",
+        type: "primer_bind",
         strand: 1,
         name: "primer1",
         start: 5,
@@ -499,7 +499,7 @@ ORIGIN
       },
       {
         notes: {},
-        type: "primer",
+        type: "primer_bind",
         strand: 1,
         name: "primer2",
         start: 17,
@@ -512,7 +512,7 @@ ORIGIN
     });
   });
 
-  it("parses a multi-seq gb with features of type primer, outputs json w/primers at top level by default", function() {
+  it("parses a multi-seq gb with features of type primer_bind, outputs json w/primers at top level by default", function() {
     const string = fs.readFileSync(
       path.join(__dirname, "./testData/genbank/testing_primers_multiseq.gb"),
       "utf8"
@@ -530,7 +530,7 @@ ORIGIN
     });
   });
 
-  it("parses a multi-seq gb with features of type primer, outputs json w/primers as features of type primer because primersAsFeatures = true",  function() {
+  it("parses a multi-seq gb with features of type primer_bind, outputs json w/primers as features of type primer_bind because primersAsFeatures = true",  function() {
     const string = fs.readFileSync(
       path.join(__dirname, "./testData/genbank/testing_primers_multiseq.gb"),
       "utf8"

diff --git a/src/test/jsonToGenbank.test.js b/src/test/jsonToGenbank.test.js
@@ -411,7 +411,7 @@ describe("genbank exporter/parser conversion", function() {
 
     result[0].parsedSequence.primers.should.containSubset([
       {
-        type: "primer",
+        type: "primer_bind",
         strand: 1,
         name: "primer_to_export",
         start: 5,

diff --git a/src/test/testData/genbank/testing_primers.gb b/src/test/testData/genbank/testing_primers.gb
@@ -2,7 +2,7 @@ LOCUS       testing_primers          27 bp    DNA     linear    25-JUL-2019
       FEATURES             Location/Qualifiers
            misc_feature    2..4
                            /label="feature1"
-           primer          6..10
+           primer_bind     6..10
                            /label="primer1"
            misc_feature    12..16
                            /label="feature2"

diff --git a/src/test/testData/genbank/testing_primers_multiseq.gb b/src/test/testData/genbank/testing_primers_multiseq.gb
@@ -2,11 +2,11 @@ LOCUS       testing_primers1          27 bp    DNA     linear    25-JUL-2019
       FEATURES             Location/Qualifiers
            misc_feature    2..4
                            /label="feature1"
-           primer          6..10
+           primer_bind     6..10
                            /label="primer1"
            misc_feature    12..16
                            /label="feature2"
-           primer          18..24
+           primer_bind     18..24
                            /label="primer2"
       ORIGIN
               1 ATGCATTGAG GACCTAACCA TATCTAA
@@ -15,7 +15,7 @@ LOCUS       testing_primers2          27 bp    DNA     linear    25-JUL-2019
       FEATURES             Location/Qualifiers
            misc_feature    2..4
                            /label="feature3"
-           primer          6..10
+           primer_bind     6..10
                            /label="primer3"
            misc_feature    12..16
                            /label="feature4"

diff --git a/yarn.lock b/yarn.lock
@@ -1053,7 +1053,7 @@ async-limiter@~1.0.0:
   resolved "https://registry.yarnpkg.com/async-limiter/-/async-limiter-1.0.1.tgz#dd379e94f0db8310b08291f9d64c3209766617fd"
   integrity sha512-csOlWGAcRFJaI6m+F2WKdnMKr4HhdhFVBk0H/QbJFMCr+uO2kwohwXQPxw/9OCxp05r5ghVBFSyioixx3gfkNQ==
 
-async@1.x, async@^1.5.0, async@^1.5.2:
+async@1.x, async@^1.5.2:
   version "1.5.2"
   resolved "https://registry.yarnpkg.com/async/-/async-1.5.2.tgz#ec6a61ae56480c0c3cb241c95618e20892f9672a"
   integrity sha1-7GphrlZIDAw8skHJVhjiCJL5Zyo=
@@ -10945,10 +10945,10 @@ ve-range-utils@^2.5.9:
     lodash "^4.17.4"
     validate.io-nonnegative-integer-array "^1.0.1"
 
-ve-sequence-utils@5.0.0:
-  version "5.0.0"
-  resolved "https://registry.yarnpkg.com/ve-sequence-utils/-/ve-sequence-utils-5.0.0.tgz#521379ca017348714476bf60f276cd220ed8ee1d"
-  integrity sha512-kQKJbiwTlxBIWbQih5tRhpmUzERPkLDnL93EJeQTXSg7LSZn0fLzjtpc3Yjuu6ok8tNLApn420e0QVbvc2b5cA==
+ve-sequence-utils@5.1.0:
+  version "5.1.0"
+  resolved "https://registry.yarnpkg.com/ve-sequence-utils/-/ve-sequence-utils-5.1.0.tgz#3a2948a71fbce7c3ff0e102760598ef3e32070ad"
+  integrity sha512-/9gHhuXjcu2gR5yCrCwy5b0ie/5r+umZDF3fJswT7uO+K6RfNEszVRKByHwOfwKCK0dgGrzs6dMaDZfRETlZdA==
   dependencies:
     bson-objectid "^1.1.1"
     escape-string-regexp "^1.0.5"