Get gene sequence

[Michał T. Lorenc]

Hi all,

Apollo allows to drag-n-drop a gene into the yellow field, and from the gene menu, you can select Get Sequence and get, for example, the peptide sequence for the gene as shown below:

The above solution works, but most users forget to delete the genes from the yellow Apollo's annotation field. Therefore, I wrote a small web app based on Python's Flask framework, which can be found here. To add it to Apollo, I need to add the following lines to trackList.json for the gene track:

{
  "menuTemplate": [
    {},
    {},
    {
      "action": "iframeDialog",
      "label": "Get Sequence",
      "title": "{Name}",
      "iconClass": "dijitIconDatabase",
      "url": "https://apollo.nbenth.com/getseq/{ID}"
    }
  ],
  "storeClass": "JBrowse/Store/SeqFeature/NCList",
  "urlTemplate": "tracks/SeqViewer-test/{refseq}/trackData.jsonz",
  "style": {
    "className": "feature"
  },
  "label": "SeqViewer-test",
  "apollo": {
    "topType": "mRNA",
    "source": "upload",
    "type": "GFF3_JSON"
  },
  "type": "JBrowse/View/Track/HTMLFeatures",
  "key": "SeqViewer-test"
}

The user needs to select a gene and click right-mouse click and select Get Sequence from the menu:

However, the problem with my solution is that I need to create a new database for each annotation. How is it possible to access Apollo's database, or how can Get Sequence be extracted from Apollo and replace my code?

I really appreciate any help you can provide.

Michal

[Michał T. Lorenc]

P.S. I added it also to [GitHub issues](https://github.com/GMOD/Apollo/issues/2643)