comparison jbrowse2/jbrowse2.py @ 2:22e3d068fdc9 draft

Uploaded

1:af3fba6c21aa

            "assemblyNames": [self.genome_name],
            "adapter": {
                "type": "Gff3TabixAdapter",
                "gffGzLocation": {"locationType": "UriLocation", "uri": url},
                "index": {
                    "location": {"locationType": "UriLocation", "uri": url + ".tbi"}
                },
            },
            "displays": [
                {
                    "type": "LinearBasicDisplay",

    def add_bed(self, data, ext, trackData):
        url = "%s.%s" % (trackData["label"], ext)
        dest = os.path.realpath("%s/%s" % (self.outdir, url))
        self._sort_bed(data, dest)
        tId = trackData["label"]
        trackDict = {
            "type": "FeatureTrack",
            "trackId": tId,
            "name": trackData["name"],
            "assemblyNames": [self.genome_name],
            "adapter": {
                "type": "BedAdapter",
                "bedLocation": {"locationType": "UriLocation", "uri": url + ".gz"},
            },
            "displays": [
                {
                    "type": "LinearBasicDisplay",
                    "displayId": "%s-LinearBasicDisplay" % tId,

2:22e3d068fdc9

            "assemblyNames": [self.genome_name],
            "adapter": {
                "type": "Gff3TabixAdapter",
                "gffGzLocation": {"locationType": "UriLocation", "uri": url},
                "index": {
                    "location": {"uri": url + ".tbi", "locationType": "UriLocation"}
                },
            },
            "displays": [
                {
                    "type": "LinearBasicDisplay",

    def add_bed(self, data, ext, trackData):
        url = "%s.%s" % (trackData["label"], ext)
        dest = os.path.realpath("%s/%s" % (self.outdir, url))
        self._sort_bed(data, dest)
        tId = trackData["label"]
        url = url + ".gz"
        trackDict = {
            "type": "FeatureTrack",
            "trackId": tId,
            "name": trackData["name"],
            "assemblyNames": [self.genome_name],
            "adapter": {
                "type": "BedTabixAdapter",
                "bedGzLocation": {"locationType": "UriLocation", "uri": url},
                "index": {
                    "location": {"uri": url + ".tbi", "locationType": "UriLocation"}
                },
            },
            "displays": [
                {
                    "type": "LinearBasicDisplay",
                    "displayId": "%s-LinearBasicDisplay" % tId,