comparison jbrowse2.py @ 78:7bb6259ea52f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty

77:3dcda36b97b4

class JbrowseConnector(object):
    def __init__(self, outdir, jbrowse2path):
        self.assemblies = []  # these require more than a few line diff.
        self.assmeta = {}
        self.ass_first_contigs = (
            []
        )  # for default session - these are read as first line of the assembly .fai
        self.giURL = GALAXY_INFRASTRUCTURE_URL
        self.outdir = outdir
        self.jbrowse2path = jbrowse2path
        os.makedirs(self.outdir, exist_ok=True)
        self.genome_names = []

            config_json = json.load(config_file)
        if self.config_json:
            config_json.update(self.config_json)
        if "defaultSession" in config_json:
            session_json = config_json["defaultSession"]
        else:
            session_json = {}
            session_views = []
        for gnome in self.genome_names:
            tracks_data = []

                    }
                )
            # paf genomes have no tracks associated so nothing for the view
            if len(tracks_data) > 0:
                view_json = {"type": "LinearGenomeView", "tracks": tracks_data}
                refName = self.assmeta[gnome][0].get("genome_firstcontig", None)
                drdict = {
                    "reversed": False,
                    "assemblyName": gnome,
                    "start": 0,
                    "end": 100000,
                    "refName": refName,
                }
                ddl = default_data.get("defaultLocation", None)
                if ddl:
                    loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl)
                    # allow commas like 100,000 but ignore as integer
                    if loc_match:
                        refName = loc_match.group(1)
                        drdict["refName"] = refName
                        if loc_match.group(2) > "":
                            drdict["start"] = int(loc_match.group(2).replace(",", ""))
                        if loc_match.group(3) > "":
                            drdict["end"] = int(loc_match.group(3).replace(",", ""))
                    else:
                        logging.info(
                            "@@@ regexp could not match contig:start..end in the supplied location %s - please fix"
                            % ddl
                        )
                if drdict.get("refName", None):
                    # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome
                    view_json["displayedRegions"] = [
                        drdict,
                    ]
                    logging.info("@@@ defaultlocation %s for default session" % drdict)
                else:
                    logging.info(
                        "@@@ no contig name found for default session - please add one!"
                    )
                session_views.append(view_json)
        session_name = default_data.get("session_name", "New session")
        for key, value in mapped_chars.items():
            session_name = session_name.replace(value, key)

        logging.debug("def ass_first=%s\ndata=%s" % (self.ass_first_contigs, data))
        for first_contig in self.ass_first_contigs:
            logging.debug("first contig=%s" % self.ass_first_contigs)
            [gnome, refName, end] = first_contig
            start = 0
            # if False or data.get("defaultLocation", ""):
                # loc_match = re.search(
                    # r"^([^:]+):([\d,]*)\.*([\d,]*)$", data["defaultLocation"]
                # )
                # # loc_match = re.search(r"^(\w+):(\d+)\.+(\d+)$", data["defaultLocation"])
                # if loc_match:
                    # refName = loc_match.group(1)
                    # start = int(loc_match.group(2))
                    # end = int(loc_match.group(3))
            # else:
            aview = {
                "assembly": gnome,
                "loc": "{}:{}..{}".format(refName, start, end),
                "type": "LinearGenomeView",
                "tracks": data[gnome]["tracks"],

    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.add_defsess_to_index(default_session_data)
    # jc.text_index() not sure what broke here.

78:7bb6259ea52f

class JbrowseConnector(object):
    def __init__(self, outdir, jbrowse2path):
        self.assemblies = []  # these require more than a few line diff.
        self.assmeta = {}
        self.ass_first_contigs = []  # for default session - these are read as first line of the assembly .fai
        self.giURL = GALAXY_INFRASTRUCTURE_URL
        self.outdir = outdir
        self.jbrowse2path = jbrowse2path
        os.makedirs(self.outdir, exist_ok=True)
        self.genome_names = []

            config_json = json.load(config_file)
        if self.config_json:
            config_json.update(self.config_json)
        if "defaultSession" in config_json:
            session_json = config_json["defaultSession"]
            session_views = []
        else:
            session_json = {}
            session_views = []
        for gnome in self.genome_names:
            tracks_data = []

                    }
                )
            # paf genomes have no tracks associated so nothing for the view
            if len(tracks_data) > 0:
                view_json = {"type": "LinearGenomeView", "tracks": tracks_data}
                logging.debug("Looking for %s in self.ass_ %s" % (gnome, self.ass_first_contigs))
                first = [x for x in self.ass_first_contigs if x[0] == gnome]
                if len(first) > 0:
                    [gnome, refName, end] = first[0]
                    start = 1
                    end = int(end)
                    refName = self.assmeta[gnome][0].get("genome_firstcontig", None)
                    drdict = {
                        "reversed": False,
                        "assemblyName": gnome,
                        "start": start,
                        "end": end,
                        "refName": refName,
                    }
                else:
                    ddl = default_data.get("defaultLocation", None)
                    if ddl:
                        loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl)
                        # allow commas like 100,000 but ignore as integer
                        if loc_match:
                            refName = loc_match.group(1)
                            drdict["refName"] = refName
                            if loc_match.group(2) > "":
                                drdict["start"] = int(loc_match.group(2).replace(",", ""))
                            if loc_match.group(3) > "":
                                drdict["end"] = int(loc_match.group(3).replace(",", ""))
                        else:
                            logging.info(
                                "@@@ regexp could not match contig:start..end in the supplied location %s - please fix"
                                % ddl
                            )
                if drdict.get("refName", None):
                    # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome
                    view_json["displayedRegions"] = [
                        drdict,
                    ]
                    logging.info("@@@ defaultlocation %s for default session" % drdict)
                else:
                    logging.info(
                        "@@@ no track location for default session - please add one!"
                    )
                session_views.append(view_json)
        session_name = default_data.get("session_name", "New session")
        for key, value in mapped_chars.items():
            session_name = session_name.replace(value, key)

        logging.debug("def ass_first=%s\ndata=%s" % (self.ass_first_contigs, data))
        for first_contig in self.ass_first_contigs:
            logging.debug("first contig=%s" % self.ass_first_contigs)
            [gnome, refName, end] = first_contig
            start = 0
            aview = {
                "assembly": gnome,
                "loc": "{}:{}..{}".format(refName, start, end),
                "type": "LinearGenomeView",
                "tracks": data[gnome]["tracks"],

    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.add_defsess_to_index(default_session_data)
    # jc.text_index() not sure what broke here.