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-- %TEACHINGWEB%.KamranAli - 08 Dec 2009

Collecting Features Using the Config File

It seems most people have been using "flatfile-to-json.pl" in order to get their feature data to JBrowse but this requires running the command for each feature you wish to specify and having to remember/store the feature specification if you wish to collect your feature data again.

Using "biodb-to-json.pl" allows you to store all your feature specifications in a single .json file. An example of such a file is volvox.json located in docs/tutorial/conf_files. Below are the contents of a simple config file 'Bovine.json' that contains just two features, "gene" and "mRNA".

{
  "description": "Bovine IV Example Database",
  "db_adaptor": "Bio::DB::SeqFeature::Store",
  "db_args": { "-adaptor": "memory",
               "-dir": "docs/tutorial/data_files" },

  "TRACK DEFAULTS": {
    "class": "feature",
    "autocomplete": "all"
  },

  "tracks": [
    {
      "track": "Genes",
      "feature": ["gene"],
      "class": "feature5",
      "key": "Protein-coding genes"
    },
    {
      "track": "ReadingFrame",
      "feature": ["mRNA"],
      "class": "dblhelix",
      "key": "Frame usage",
      "category": "Genes"
    }
  ]
}

Instead of accesing an annotation database,"db_adaptor" and "db_args" at the top will load your annotations in your gff into memory.

After running "prepare-refseqs.pl", all the feature data can be collected by running "biodb-to-json.pl --conf Bovin.json"

This isn't very useful when there's only two tracks you want to display but as your annotations grow it's a lot easier to just add the new track specifications to the config file. Also if you're going to be annotating multiple genomes with different feature sets you can just collect all the track specifications in one file and use the same config file for each genome. This will help keep your track visualizations consistent and make your life easier by keeping everything in one place.

If you have any questions send me an email and if anyone is interested I can upload the config file my group is using for the retrovirus.

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