GMOD / jbrowse-plugin-msaview

multiple sequence alignment browser plugin for JBrowse 2
Apache License 2.0
3 stars 0 forks source link

Create a config schema to map tracks to a MSA location, to help bridge LGV and MSA views #25

Open cmdcolin opened 3 years ago

cmdcolin commented 3 years ago

A config.json file may have something like this

diff --git a/test_data/config_demo.json b/test_data/config_demo.json
index 42b82a680..80218c1a1 100644
--- a/test_data/config_demo.json
+++ b/test_data/config_demo.json
@@ -72,6 +72,11 @@
       }
     }
   ],
+  "configuration": {
+    "msaView": {
+      "ncbi_gff_hg19": "msaView_{geneName}.msa"
+    }
+  },
   "tracks": [
     {
       "type": "FeatureTrack",

This would allow the msaview to know that the ncbi_gffhg19 track is associated with msa files with the format msaView{geneName}.msa or some similar remote API with a format like this e.g. rest.ensembl.org/msa/?gene={geneName}

It would be difficult to add this information directly to the track config itself, because it would need a separate config slot, but having it as a top level config with trackId->msa mappings may help