jbrowse pythium conf

pythium.conf

{
  "description": "Pythium",
  "db_adaptor": "Bio::DB::Das::Chado",
  "db_args": { "-dsn": "dbi:Pg:dbname=chado",
               "-user": "gmod",
               "-pass": ""},

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

  "tracks": [
    {
      "track": "Genes",
      "feature": ["gene"],
      "class": "feature5",
      "key": "Protein-coding genes"
    },
    {
      "track": "Transcript",
      "feature": ["mRNA"],
      "description": 1,
      "class": "transcript",
      "subfeatures": true,
      "subfeature_classes": {
        "exon": "transcript-exon",
        "CDS": "transcript-CDS",
        "UTR": "transcript-UTR"
      },
      "arrowheadClass": "transcript-arrowhead",
      "key": "Exonerate predictions",
      "category": "Genes"
    },
    {
      "track": "FGENESH",
      "feature": ["match:fgenesh", "match:fgenesh_masked"],
      "description": 1,
      "class": "transcript",
      "subfeatures": true,
      "subfeature_classes": {
        "match_part": "transcript-CDS"
      },
      "arrowheadClass": "transcript-arrowhead",
      "key": "FGENESH predictions",
      "category": "Gene-predictions"
    },
    {
      "track": "SNAP",
      "feature": ["match:snap", "match:snap_masked"],
      "description": 1,
      "class": "transcript",
      "subfeatures": true,
      "subfeature_classes": {
        "match_part": "transcript-CDS"
      },
      "arrowheadClass": "transcript-arrowhead",
      "key": "SNAP predictions",
      "category": "Gene-predictions"
    },
    {
      "track": "GeneMark",
      "feature": ["match:genemark", "match:genemark_masked"],
      "description": 1,
      "class": "transcript",
      "subfeatures": true,
      "subfeature_classes": {
        "match_part": "transcript-CDS"
      },
      "arrowheadClass": "transcript-arrowhead",
      "key": "GeneMark predictions",
      "category": "Gene-predictions"
    },
    {
      "track": "Augustus",
      "feature": ["match:augustus", "match:augustus_masked"],
      "description": 1,
      "class": "transcript",
      "subfeatures": true,
      "subfeature_classes": {
        "match_part": "transcript-CDS"
      },
      "arrowheadClass": "transcript-arrowhead",
      "key": "Augustus predictions",
      "category": "Gene-predictions"
    },
    {
      "track": "RepeatMasker",
      "feature": ["match:repeatmasker"],
      "class": "generic_parent",
      "subfeatures": true,
      "subfeature_classes": {
        "match_part": "match_part"
      },
      "key": "BLASTX RepeatRunner repeat",
      "category": "repeats"
    },
    {
      "track": "BLASTX",
      "feature": ["protein_match:blastx", "match:blastx"],
      "class": "generic_parent",
      "subfeatures": true,
      "subfeature_classes": {
        "match_part": "match_part"
      },
      "key": "BLASTX protein evidence alignment",
      "category": "protein evidence"
    },
    {
      "track": "protein2genome",
      "feature": ["protein_match:protein2genome", "match:protein2genome"],
      "class": "generic_parent",
      "subfeatures": true,
      "subfeature_classes": {
        "match_part": "match_part"
      },
      "key": "Exonerate protein evidence alignment",
      "category": "protein evidence"
    },
    {
      "track": "BLASTN",
      "feature": ["expressed_sequence_match:blastn", "nucleotide_match:blastn", "match:blastn"],
      "class": "generic_parent",
      "subfeatures": true,
      "subfeature_classes": {
        "match_part": "match_part"
      },
      "key": "BLASTN EST evidence alignment",
      "category": "EST evidence"
    },
    {
      "track": "TBLASTX",
      "feature": ["expressed_sequence_match:tblastx", "nucleotide_match:tblastx", "match:tblastx"],
      "class": "generic_parent",
      "subfeatures": true,
      "subfeature_classes": {
        "match_part": "match_part"
      },
      "key": "TBLASTN alt-EST evidence alignment",
      "category": "EST evidence"
    },
    {
      "track": "est2genome",
      "feature": ["expressed_sequence_match:est2genome", "nucleotide_match:est2genome", "match:est2genome"],
      "class": "generic_parent",
      "subfeatures": true,
      "subfeature_classes": {
        "match_part": "match_part"
      },
      "key": "Exonerate EST evidence alignment",
      "category": "EST evidence"
    }
  ]
}