comparison jbrowse2.py @ 13:1d86925dbb4c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty

12:247e17ce504b

        view_json = {"type": "LinearGenomeView", "tracks": tracks_data}

        refName = None
        if data.get("defaultLocation", ""):
            ddl = data["defaultLocation"]
            loc_match = re.search(r"^(\w.+):(\d+)\.+(\d+)$", ddl)
            if loc_match:
                refName = loc_match.group(1)
                start = int(loc_match.group(2))
                end = int(loc_match.group(3))
            else:

        elif self.genome_name is not None:
            refName = self.genome_name
            start = 0
            end = 10000  # Booh, hard coded! waiting for https://github.com/GMOD/jbrowse-components/issues/2708
            logging.info(
                "@@@ no defaultlocation found for default session - suggest adding one!"
            )

        if refName is not None:
            # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome
            view_json["displayedRegions"] = [

                "@@@ defaultlocation %s for default session"
                % view_json["displayedRegions"]
            )
        else:
            logging.info(
                "@@@ no assembly name found default session - suggest adding one!"
            )
        session_name = data.get("session_name", "New session")
        for key, value in mapped_chars.items():
            session_name = session_name.replace(value, key)
        # Merge with possibly existing defaultSession (if upgrading a jbrowse instance)

13:1d86925dbb4c

        view_json = {"type": "LinearGenomeView", "tracks": tracks_data}

        refName = None
        if data.get("defaultLocation", ""):
            ddl = data["defaultLocation"]
            loc_match = re.search(
                r"^([^:]+):(\d+)\.+(\d+)$", ddl
            )  # was re.search(r"^(\w.+):(\d+)\.+(\d+)$"
            if loc_match:
                refName = loc_match.group(1)
                start = int(loc_match.group(2))
                end = int(loc_match.group(3))
            else:

        elif self.genome_name is not None:
            refName = self.genome_name
            start = 0
            end = 10000  # Booh, hard coded! waiting for https://github.com/GMOD/jbrowse-components/issues/2708
            logging.info(
                "@@@ no defaultlocation found for default session - please add one"
            )

        if refName is not None:
            # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome
            view_json["displayedRegions"] = [

                "@@@ defaultlocation %s for default session"
                % view_json["displayedRegions"]
            )
        else:
            logging.info(
                "@@@ no contig name found for default session - please add one!"
            )
        session_name = data.get("session_name", "New session")
        for key, value in mapped_chars.items():
            session_name = session_name.replace(value, key)
        # Merge with possibly existing defaultSession (if upgrading a jbrowse instance)