comparison jbrowse2.py @ 79:14ecbe46ae9f draft

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

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 = []

                        "displays": [style_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"

        with open(self.config_json_file, "w") as config_file:
            json.dump(self.config_json, config_file, indent=2)

    def add_defsess_to_index(self, data):
        """
        Broken in Anthony's PR because only ever dealt with the first assembly.

        Add some default session settings: set some assemblies/tracks on/off

        This allows to select a default view:
        - jb type (Linear, Circular, etc)
        - default location on an assembly

    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.

79:14ecbe46ae9f

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 = []

                        "displays": [style_data],
                    }
                )
            # paf genomes have no tracks associated so nothing for the view
            if len(tracks_data) > 0:
                view_json = {
                    "type": "LinearGenomeView",
                    "offsetPx": 0,
                    "minimized": False,
                    "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 = 0
                    end = int(end)
                    refName = self.assmeta[gnome][0].get("genome_firstcontig", None)
                    drdict = {
                        "refName": refName,
                        "start": start,
                        "end": end,
                        "reversed": False,
                        "assemblyName": gnome,
                    }
                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"

        with open(self.config_json_file, "w") as config_file:
            json.dump(self.config_json, config_file, indent=2)

    def add_defsess_to_index(self, data):
        """
        This was included on request of the new codeowner from Anthony's IUC PR.
        Now fixed to deal with each assembly and tracks separately.
        Originally used only the first assembly, putting all tracks there and
        generally falling apart when tested with 2 or more. Seems ironic that
        this vital feature was never tested given the rejection of my original IUC PR
        because it was not there. And no, reviewer, I do not want this important piece of history
        removed. I prefer that it remain here since it has caused me considerable discomfort.

         ----------------------------------------------------------
        Add some default session settings: set some assemblies/tracks on/off

        This allows to select a default view:
        - jb type (Linear, Circular, etc)
        - default location on an assembly

    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)
    # note that this can be left in the config.json but has NO EFFECT if add_defsess_to_index is called.
    jc.add_defsess_to_index(default_session_data)
    # jc.text_index() not sure what broke here.