[skip ci] Human vs mouse synteny

GMOD · Jan 9, 2023 · cf5522e · cf5522e
1 parent aa43be2
commit cf5522e
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Showing 2 changed files with 108 additions and 7 deletions.
diff --git a/plugins/gtf/src/GtfAdapter/GtfAdapter.ts b/plugins/gtf/src/GtfAdapter/GtfAdapter.ts
@@ -84,13 +84,14 @@ export default class extends BaseFeatureDataAdapter {
     }) as FeatureLoc[][]
 
     const intervalTree = new IntervalTree()
-    const ret = data.flat().map(
-      (f, i) =>
-        new SimpleFeature({
-          data: featureData(f),
-          id: `${this.id}-${refName}-${i}`,
-        }),
-    )
+    const ret = data.flat().map((f, i) => {
+      const data = featureData(f)
+      return new SimpleFeature({
+        // @ts-ignore
+        data: { ...data, name: data.gene_name },
+        id: `${this.id}-${refName}-${i}`,
+      })
+    })
 
     for (let i = 0; i < ret.length; i++) {
       const obj = ret[i]

diff --git a/test_data/human_vs_mouse.json b/test_data/human_vs_mouse.json
@@ -0,0 +1,100 @@
+{
+  "assemblies": [
+    {
+      "name": "hs1",
+      "sequence": {
+        "type": "ReferenceSequenceTrack",
+        "trackId": "hs1-ReferenceSequenceTrack",
+        "adapter": {
+          "type": "TwoBitAdapter",
+          "twoBitLocation": {
+            "uri": "https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/hs1.2bit"
+          },
+          "chromSizesLocation": {
+            "uri": "https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/hs1.chrom.sizes.txt"
+          }
+        }
+      }
+    },
+    {
+      "name": "mm39",
+      "sequence": {
+        "type": "ReferenceSequenceTrack",
+        "trackId": "mm39-ReferenceSequenceTrack",
+        "adapter": {
+          "type": "TwoBitAdapter",
+          "twoBitLocation": {
+            "uri": "https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.2bit"
+          },
+          "chromSizesLocation": {
+            "uri": "https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.chrom.sizes"
+          }
+        }
+      }
+    }
+  ],
+  "configuration": {},
+  "connections": [],
+  "defaultSession": {
+    "name": "New Session"
+  },
+  "tracks": [
+    {
+      "type": "FeatureTrack",
+      "trackId": "liftoff_genes",
+      "name": "liftOff genes",
+      "assemblyNames": ["hs1"],
+      "category": ["Annotation"],
+      "adapter": {
+        "type": "GtfAdapter",
+        "gtfLocation": {
+          "uri": "https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/genes/catLiftOffGenesV1.gtf.gz",
+          "locationType": "UriLocation"
+        }
+      }
+    },
+    {
+      "type": "FeatureTrack",
+      "trackId": "refgene",
+      "name": "refGene",
+      "assemblyNames": ["mm39"],
+      "category": ["Annotation"],
+      "adapter": {
+        "type": "GtfAdapter",
+        "gtfLocation": {
+          "uri": "https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/genes/refGene.gtf.gz",
+          "locationType": "UriLocation"
+        }
+      }
+    },
+
+    {
+      "type": "FeatureTrack",
+      "trackId": "ncbiRefSeq",
+      "name": "ncbiRefSeq",
+      "adapter": {
+        "type": "BigBedAdapter",
+        "bigBedLocation": {
+          "uri": "https://hgdownload.soe.ucsc.edu/gbdb/hs1/bbi/ncbiRefSeq.bb",
+          "locationType": "UriLocation"
+        }
+      },
+      "assemblyNames": ["hs1"]
+    },
+    {
+      "type": "SyntenyTrack",
+      "trackId": "liftover",
+      "name": "liftover",
+      "adapter": {
+        "type": "ChainAdapter",
+        "chainLocation": {
+          "uri": "https://hgdownload.soe.ucsc.edu/goldenPath/hs1/liftOver/hs1ToMm39.over.chain.gz",
+          "locationType": "UriLocation"
+        },
+        "targetAssembly": "hs1",
+        "queryAssembly": "mm39"
+      },
+      "assemblyNames": ["hs1", "mm39"]
+    }
+  ]
+}