comparison jbrowse2.py @ 71:e26a8a6d2d2e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cf208cecf0140ff43d145a44713ab7108057fb8b

70:5f0ee87daef4

    def __init__(self, outdir, jbrowse2path):
        self.assemblies = []  # these require more than a few line diff.
        self.assmeta = {}
        self.giURL = GALAXY_INFRASTRUCTURE_URL
        self.outdir = outdir
        self.genome_firstcontig = None
        self.jbrowse2path = jbrowse2path
        os.makedirs(self.outdir, exist_ok=True)
        self.genome_names = []
        self.trackIdlist = []
        self.tracksToAdd = {}

            lab = trackData["label"]
            if len(gname.split()) > 1:
                gname = gname.split()[0]
            passnames.append(gname)
            # trouble from spacey names in command lines avoidance
            if gname not in self.genome_names:
                # ignore if already there - eg for duplicates among pafs.
                useuri = pgpaths[i].startswith("http://") or pgpaths[i].startswith(
                    "https://"
                )
                asstrack = self.make_assembly(pgpaths[i], gname, useuri)
                self.genome_names.append(gname)
                self.tracksToAdd[gname] = []
                self.assemblies.append(asstrack)
                if not useuri:
                    url = "%s.paf" % (lab)
                    dest = "%s/%s" % (self.outdir, url)
                    self.symlink_or_copy(os.path.realpath(data), dest)
                else:
                    url = data
        trackDict = {
            "type": "SyntenyTrack",
            "trackId": tId,
            "assemblyNames": passnames,
            "category": [

                        item.tag: parse_style_conf(item)
                        for item in track.find("options/style")
                    }
                else:
                    default_session_data["style"][key] = {}
                    logging.warn("@@@@ no options/style found for %s" % (key))

                if track.find("options/style_labels"):
                    default_session_data["style_labels"][key] = {
                        item.tag: parse_style_conf(item)
                        for item in track.find("options/style_labels")

        "quaternary_color": root.find("metadata/general/quaternary_color").text,
        "font_size": root.find("metadata/general/font_size").text,
    }
    jc.add_general_configuration(general_data)
    trackconf = jc.config_json.get("tracks", [])
    logging.warn("++++++++++++ genome_names=%s" % jc.genome_names)
    for gnome in jc.genome_names:
        trackconf += jc.tracksToAdd[gnome]
    jc.config_json["tracks"] = trackconf
    assconf = jc.config_json.get("assemblies", [])
    assconf += jc.assemblies
    jc.config_json["assemblies"] = assconf
    logging.warn("&&&assemblies=%s, gnames=%s" % (assconf, jc.genome_names))
    jc.write_config()
    jc.add_default_session(default_session_data)
    # jc.text_index() not sure what broke here.

71:e26a8a6d2d2e

    def __init__(self, outdir, jbrowse2path):
        self.assemblies = []  # these require more than a few line diff.
        self.assmeta = {}
        self.giURL = GALAXY_INFRASTRUCTURE_URL
        self.outdir = outdir
        self.jbrowse2path = jbrowse2path
        os.makedirs(self.outdir, exist_ok=True)
        self.genome_names = []
        self.trackIdlist = []
        self.tracksToAdd = {}

            lab = trackData["label"]
            if len(gname.split()) > 1:
                gname = gname.split()[0]
            passnames.append(gname)
            # trouble from spacey names in command lines avoidance
            useuri = pgpaths[i].startswith("http://") or pgpaths[i].startswith(
                "https://"
            )
            if not useuri:
                url = "%s.paf" % (lab)
            else:
                url = data
            if gname not in self.genome_names:
                # ignore if already there - eg for duplicates among pafs.
                asstrack = self.make_assembly(pgpaths[i], gname, useuri)
                self.genome_names.append(gname)
                self.tracksToAdd[gname] = []
                self.assemblies.append(asstrack)
                if not useuri:
                    dest = "%s/%s" % (self.outdir, url)
                    self.symlink_or_copy(os.path.realpath(data), dest)
        trackDict = {
            "type": "SyntenyTrack",
            "trackId": tId,
            "assemblyNames": passnames,
            "category": [

                        item.tag: parse_style_conf(item)
                        for item in track.find("options/style")
                    }
                else:
                    default_session_data["style"][key] = {}
                    logging.debug("@@@@ no options/style found for %s" % (key))

                if track.find("options/style_labels"):
                    default_session_data["style_labels"][key] = {
                        item.tag: parse_style_conf(item)
                        for item in track.find("options/style_labels")

        "quaternary_color": root.find("metadata/general/quaternary_color").text,
        "font_size": root.find("metadata/general/font_size").text,
    }
    jc.add_general_configuration(general_data)
    trackconf = jc.config_json.get("tracks", [])
    for gnome in jc.genome_names:
        trackconf += jc.tracksToAdd[gnome]
    jc.config_json["tracks"] = trackconf
    assconf = jc.config_json.get("assemblies", [])
    assconf += jc.assemblies
    jc.config_json["assemblies"] = assconf
    logging.debug("&&&assemblies=%s, gnames=%s" % (assconf, jc.genome_names))
    jc.write_config()
    jc.add_default_session(default_session_data)
    # jc.text_index() not sure what broke here.