comparison jbrowse2.py @ 12:247e17ce504b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4baeb144cafbb61ae0587cce731066129097c168-dirty

11:f5ce31c2f47d

        # The view for the assembly we're adding
        view_json = {"type": "LinearGenomeView", "tracks": tracks_data}

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

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

                    "reversed": False,
                    "assemblyName": self.genome_name,
                }
            ]

        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)
        session_json = {}

12:247e17ce504b

        # The view for the assembly we're adding
        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:
                logging.info(
                    "@@@ regexp could not match contig:start..end in the supplied location %s - please fix"
                    % ddl
                )
        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"] = [
                {

                    "reversed": False,
                    "assemblyName": self.genome_name,
                }
            ]

            logging.info(
                "@@@ 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)
        session_json = {}