Disable resolution of Derives_from fields in GFF3 parsing, fixes TAIR…

… gff (#3272)
GMOD · Oct 19, 2022 · f96ec17 · f96ec17
1 parent cb9159a
commit f96ec17
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Showing 6 changed files with 18 additions and 7 deletions.
diff --git a/plugins/gff3/package.json b/plugins/gff3/package.json
@@ -39,7 +39,7 @@
   "dependencies": {
     "@flatten-js/interval-tree": "^1.0.15",
     "@gmod/bgzf-filehandle": "^1.4.3",
-    "@gmod/gff": "^1.2.0",
+    "@gmod/gff": "^1.2.3",
     "@gmod/tabix": "^1.5.2"
   },
   "peerDependencies": {

diff --git a/plugins/gff3/src/Gff3Adapter/Gff3Adapter.ts b/plugins/gff3/src/Gff3Adapter/Gff3Adapter.ts
@@ -42,6 +42,7 @@ export default class extends BaseFeatureDataAdapter {
       parseComments: false,
       parseDirectives: false,
       parseSequences: false,
+      disableDerivesFromReferences: true,
     })
 
     const intervalTree = feats
@@ -158,7 +159,7 @@ export default class extends BaseFeatureDataAdapter {
 
     delete f.child_features
     delete f.data
-    delete f.derived_features
+    // delete f.derived_features
     delete f.attributes
     delete f.seq_id
     return f

diff --git a/plugins/gff3/src/Gff3Adapter/__snapshots__/Gff3Adapter.test.ts.snap b/plugins/gff3/src/Gff3Adapter/__snapshots__/Gff3Adapter.test.ts.snap
@@ -3,6 +3,7 @@
 exports[`adapter can fetch features from volvox.gff3 test getfeatures on gff plain text adapter 1`] = `
 Array [
   Object {
+    "derived_features": Array [],
     "end": 6079,
     "name": "ctgB",
     "phase": 0,
@@ -14,6 +15,7 @@ Array [
     "uniqueId": "test-offset-187",
   },
   Object {
+    "derived_features": Array [],
     "end": 1984,
     "name": "f07",
     "note": "This is an example",
@@ -26,6 +28,7 @@ Array [
     "uniqueId": "test-offset-188",
   },
   Object {
+    "derived_features": Array [],
     "end": 6130,
     "name": "f06",
     "note": "This is another example",
@@ -38,6 +41,7 @@ Array [
     "uniqueId": "test-offset-189",
   },
   Object {
+    "derived_features": Array [],
     "end": 5968,
     "name": "f05",
     "note": "ああ、この機能は、世界中を旅しています！",

diff --git a/plugins/gff3/src/Gff3TabixAdapter/Gff3TabixAdapter.ts b/plugins/gff3/src/Gff3TabixAdapter/Gff3TabixAdapter.ts
@@ -141,6 +141,7 @@ export default class extends BaseFeatureDataAdapter {
         parseComments: false,
         parseDirectives: false,
         parseSequences: false,
+        disableDerivesFromReferences: true,
       })
 
       features.forEach(featureLocs =>
@@ -247,10 +248,11 @@ export default class extends BaseFeatureDataAdapter {
 
     delete f.child_features
     delete f.data
-    delete f.derived_features
+    // delete f.derived_features
     delete f._linehash
     delete f.attributes
     delete f.seq_id
+
     return f
   }
 

diff --git a/plugins/gff3/src/Gff3TabixAdapter/__snapshots__/Gff3TabixAdapter.test.ts.snap b/plugins/gff3/src/Gff3TabixAdapter/__snapshots__/Gff3TabixAdapter.test.ts.snap
@@ -3,6 +3,7 @@
 exports[`adapter can fetch features from volvox.gff3 test getfeatures on gff plain text adapter 1`] = `
 Array [
   Object {
+    "derived_features": Array [],
     "end": 6079,
     "name": "ctgB",
     "phase": 0,
@@ -14,6 +15,7 @@ Array [
     "uniqueId": "test-offset-794327",
   },
   Object {
+    "derived_features": Array [],
     "end": 1984,
     "name": "f07",
     "note": "This is an example",
@@ -26,6 +28,7 @@ Array [
     "uniqueId": "test-offset-794370",
   },
   Object {
+    "derived_features": Array [],
     "end": 6130,
     "name": "f06",
     "note": "This is another example",
@@ -38,6 +41,7 @@ Array [
     "uniqueId": "test-offset-794439",
   },
   Object {
+    "derived_features": Array [],
     "end": 5968,
     "name": "f05",
     "note": "ああ、この機能は、世界中を旅しています！",

diff --git a/yarn.lock b/yarn.lock
@@ -1596,10 +1596,10 @@
     pump "^3.0.0"
     split2 "^4.1.0"
 
-"@gmod/gff@^1.2.0":
-  version "1.2.1"
-  resolved "https://registry.yarnpkg.com/@gmod/gff/-/gff-1.2.1.tgz#4d1e3694f2268215aa6c7bad366be84a1449034d"
-  integrity sha512-YUqPOfoaSfVVXs3Unwph4Ap3NxQIghNtNm+57DEhf+cMeUloFU6v44dKwSUcZZ+PBgAop1BD11QUVSVzmSqNgQ==
+"@gmod/gff@^1.2.3":
+  version "1.2.3"
+  resolved "https://registry.yarnpkg.com/@gmod/gff/-/gff-1.2.3.tgz#ae057592a14e3cd73a0ae430e94aa6a49e4312ca"
+  integrity sha512-ONnS+otYGLmrcd/c+j8IwRfm/gw0kWNxUOpGMap5G860LlFMYr4ltlQYucnTXDXnhcUsQHJlgLrQYhBnHf4y6A==
 
 "@gmod/gtf@^0.0.6":
   version "0.0.6"