comparison jbrowse2.py @ 101:e4ba5f1da6ef draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty

100:666c07b60cd2

    return metadata


class JbrowseConnector(object):
    def __init__(self, outdir, jbrowse2path):
        self.trackCounter = 0  # to avoid name clashes
        self.assemblies = []  # these require more than a few line diff.
        self.assmeta = {}
        self.ass_first_contigs = (
            []

        default session settings are hard and fragile.
        .add_default_view() and other configuration code adapted from
         https://github.com/abretaud/tools-iuc/blob/jbrowse2/tools/jbrowse2/jbrowse2.py
        """
        # TODO using the default session for now, but check out session specs in the future https://github.com/GMOD/jbrowse-components/issues/2708
        bpPerPx = 50 # this is tricky since browser window width is unknown - this seems a compromise that sort of works....
        track_types = {}
        with open(self.config_json_file, "r") as config_file:
            config_json = json.load(config_file)
        if self.config_json:
            config_json.update(self.config_json)

                    )

            track_conf["category"] = track.attrib["cat"]
            track_conf["format"] = track.attrib["format"]
            track_conf["conf"] = etree_to_dict(track.find("options"))
            keys = jc.process_annotations(track_conf)
            if keys:
                for key in keys:
                    vis = track.attrib.get("visibility", "default_off")
                    if not vis:

    default_session_data["session_name"] = root.find(
        "metadata/general/session_name"
    ).text
    logging.debug("default_session=%s" % (json.dumps(default_session_data, indent=2)))
    jc.zipOut = root.find("metadata/general/zipOut").text == "true"
    general_data = {
        "analytics": root.find("metadata/general/analytics").text,
        "primary_color": root.find("metadata/general/primary_color").text,
        "secondary_color": root.find("metadata/general/secondary_color").text,
        "tertiary_color": root.find("metadata/general/tertiary_color").text,

101:e4ba5f1da6ef

    return metadata


class JbrowseConnector(object):
    def __init__(self, outdir, jbrowse2path):
        self.bpPerPx = 50
        self.trackCounter = 0  # to avoid name clashes
        self.assemblies = []  # these require more than a few line diff.
        self.assmeta = {}
        self.ass_first_contigs = (
            []

        default session settings are hard and fragile.
        .add_default_view() and other configuration code adapted from
         https://github.com/abretaud/tools-iuc/blob/jbrowse2/tools/jbrowse2/jbrowse2.py
        """
        # TODO using the default session for now, but check out session specs in the future https://github.com/GMOD/jbrowse-components/issues/2708
        bpPerPx = self.bpPerPx # Browser window width is unknown and apparently cannot be figured out in JB2 code so could be 200-2000+ pixels.
        track_types = {}
        with open(self.config_json_file, "r") as config_file:
            config_json = json.load(config_file)
        if self.config_json:
            config_json.update(self.config_json)

                    )

            track_conf["category"] = track.attrib["cat"]
            track_conf["format"] = track.attrib["format"]
            track_conf["conf"] = etree_to_dict(track.find("options"))
            logging
            keys = jc.process_annotations(track_conf)
            if keys:
                for key in keys:
                    vis = track.attrib.get("visibility", "default_off")
                    if not vis:

    default_session_data["session_name"] = root.find(
        "metadata/general/session_name"
    ).text
    logging.debug("default_session=%s" % (json.dumps(default_session_data, indent=2)))
    jc.zipOut = root.find("metadata/general/zipOut").text == "true"
    jc.bpPerPx = root.find("metadata/general/bpPerPx").text
    general_data = {
        "analytics": root.find("metadata/general/analytics").text,
        "primary_color": root.find("metadata/general/primary_color").text,
        "secondary_color": root.find("metadata/general/secondary_color").text,
        "tertiary_color": root.find("metadata/general/tertiary_color").text,