comparison jbrowse2.py @ 112:56f9a6e0fe80 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 566509061b742b73c8dd1a1db6813fbf6a7a3792

111:0a532764dcfa

                }
            ]
        }
        categ = trackData["category"]
        fname = tId
        dest = "%s/%s" % (self.outdir, fname)
        gname = trackData["assemblyNames"]

        cmd = [
            "bash",
            os.path.join(INSTALLED_TO, "convertMAF.sh"),

        trackDict["style"] = style_json
        self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict))
        self.trackIdlist.append(tId)

    def add_bed(self, data, ext, trackData):
        bedPlugin = {"name": "BedScorePlugin", "umdLoc": { "uri": "bedscoreplugin.js" } }
        tId = trackData["label"]
        categ = trackData["category"]
        useuri = trackData["useuri"].lower() == "yes"
        if useuri:
            url = data
        else:
            url = tId + ".gz"
            dest = os.path.join(self.outdir, url)
            self._sort_bed(data, dest)
        if True or trackData.get("usebedscore",None):
            bedgzlocation = {
                    "uri": url,
                    "columnNames": ["chr","start","end","name","score"],
                    "scoreColumn": "score",
                }
        else:
            bedgzlocation = {
                    "uri": url,
                }
        trackDict = {
            "type": "FeatureTrack",
            "trackId": tId,
            "name": trackData["name"],
            "assemblyNames": [trackData["assemblyNames"]],

                    "type": "LinearBasicDisplay",
                    "displayId": "%s-LinearBasicDisplay" % tId,
                    "renderer": {
                        "type": "SvgFeatureRenderer",
                        "color1": "jexl:customColor(feature)",
                        },
                },
                {
                    "type": "LinearPileupDisplay",
                    "displayId": "%s-LinearPileupDisplay" % tId,
                },

                passnames.append(gname)
            useuri = pafOpts["useuri"] == "true"
            if gname not in self.genome_names:
                # ignore if already there - eg for duplicates among pafs.
                asstrack, first_contig = self.make_assembly(gpath, gname, useuri)
                self.genome_names.append(copy.copy(gname))
                self.tracksToAdd[gname] = []
                self.assemblies.append(copy.copy(asstrack))
                self.ass_first_contigs.append(copy.copy(first_contig))
        trackDict = {
            "type": "SyntenyTrack",

    def process_annotations(self, track):
        category = track["category"].replace("__pd__date__pd__", TODAY)
        tt1 = ",/ :;\\"
        tt2 = "______"
        labttab = str.maketrans(tt1,tt2)
        for trackIndex, (
            dataset_path,
            dataset_ext,
            useuri,
            track_human_label,

                    track["conf"]["options"]["paf"],
                )
            else:
                logging.warning("Do not know how to handle %s", dataset_ext)
            # Return non-human label for use in other fields
            logging.debug("### processanno ext=%s trackstoadd = %s" % (dataset_ext, self.tracksToAdd))
            yield outputTrackConfig["label"]

    def add_default_session(self, default_data):
        """
        default session settings are hard and fragile.
        .add_default_view() and other configuration code adapted from
         https://github.com/abretaud/tools-iuc/blob/jbrowse2/tools/jbrowse2/jbrowse2.py
        """
        # TODO using the default session for now, but check out session specs in the future https://github.com/GMOD/jbrowse-components/issues/2708
        bpPerPx = self.bpPerPx # Browser window width is unknown and default session cannot be used to figure it out in JB2 code so could be 200-2000+ pixels.
        track_types = {}
        with open(self.config_json_file, "r") as config_file:
            config_json = json.load(config_file)
        if self.config_json:
            config_json.update(self.config_json)

                    else:
                        logging.debug(
                            "style data for %s = %s"
                            % (tId, style_data)
                        )
                    if style_data.get('type',None) == None:
                        style_data["type"] = "LinearBasicDisplay"
                    if "displays" in track_conf:
                        disp = track_conf["displays"][0]["type"]
                        style_data["type"] = disp
                    if track_conf.get("displays", None):

                            "displays": [style_data],
                        }
                    )
            first = [x for x in self.ass_first_contigs if x[0] == gnome]
            drdict = {
                    "reversed": False,
                    "assemblyName": gnome,
                }
            if len(first) > 0:
                [gnome, refName, end] = first[0]
                drdict["refName"] = refName
                drdict["start"] = 0
                end = int(end)
                drdict["end"] = end        
            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(",", ""))

                            % ddl
                        )
            view_json = {
                "type": "LinearGenomeView",
                "offsetPx": 0,
                "bpPerPx" : bpPerPx,
                "minimized": False,
                "tracks": tracks_data
            }
            if drdict.get("refName", None):
                # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome

            trackfiles = track.findall("files/trackFile")
            if trackfiles:
                for x in trackfiles:
                    isBed = False
                    if x.attrib['ext'] == "bed":
                        isBed = True                   
                    track_conf["label"] = "%s_%d" % (
                        x.attrib["label"].replace(" ", "_").replace(",", "_").replace("/","_"),
                        trackI,
                    )
                    trackI += 1
                    track_conf["useuri"] = x.attrib["useuri"]
                    if is_multi_bigwig:

112:56f9a6e0fe80

                }
            ]
        }
        categ = trackData["category"]
        fname = tId
        dest = os.path.join(self.outdir, fname)
        gname = trackData["assemblyNames"]

        cmd = [
            "bash",
            os.path.join(INSTALLED_TO, "convertMAF.sh"),

        trackDict["style"] = style_json
        self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict))
        self.trackIdlist.append(tId)

    def add_bed(self, data, ext, trackData):
        bedPlugin = {"name": "BedScorePlugin", "umdLoc": {"uri": "bedscoreplugin.js"}}
        tId = trackData["label"]
        categ = trackData["category"]
        useuri = trackData["useuri"].lower() == "yes"
        if useuri:
            url = data
        else:
            url = tId + ".gz"
            dest = os.path.join(self.outdir, url)
            self._sort_bed(data, dest)
        if True or trackData.get("usebedscore", None):
            bedgzlocation = {
                "uri": url,
                "columnNames": ["chr", "start", "end", "name", "score"],
                "scoreColumn": "score",
            }
        else:
            bedgzlocation = {
                "uri": url,
            }
        trackDict = {
            "type": "FeatureTrack",
            "trackId": tId,
            "name": trackData["name"],
            "assemblyNames": [trackData["assemblyNames"]],

                    "type": "LinearBasicDisplay",
                    "displayId": "%s-LinearBasicDisplay" % tId,
                    "renderer": {
                        "type": "SvgFeatureRenderer",
                        "color1": "jexl:customColor(feature)",
                    },
                },
                {
                    "type": "LinearPileupDisplay",
                    "displayId": "%s-LinearPileupDisplay" % tId,
                },

                passnames.append(gname)
            useuri = pafOpts["useuri"] == "true"
            if gname not in self.genome_names:
                # ignore if already there - eg for duplicates among pafs.
                asstrack, first_contig = self.make_assembly(gpath, gname, useuri)
                self.genome_names.append(gname)
                self.tracksToAdd[gname] = []
                self.assemblies.append(copy.copy(asstrack))
                self.ass_first_contigs.append(copy.copy(first_contig))
        trackDict = {
            "type": "SyntenyTrack",

    def process_annotations(self, track):
        category = track["category"].replace("__pd__date__pd__", TODAY)
        tt1 = ",/ :;\\"
        tt2 = "______"
        labttab = str.maketrans(tt1, tt2)
        for trackIndex, (
            dataset_path,
            dataset_ext,
            useuri,
            track_human_label,

                    track["conf"]["options"]["paf"],
                )
            else:
                logging.warning("Do not know how to handle %s", dataset_ext)
            # Return non-human label for use in other fields
            yield outputTrackConfig["label"]

    def add_default_session(self, default_data):
        """
        default session settings are hard and fragile.
        .add_default_view() and other configuration code adapted from
         https://github.com/abretaud/tools-iuc/blob/jbrowse2/tools/jbrowse2/jbrowse2.py
        """
        #  TODO using the default session for now, but check out session specs in the future https://github.com/GMOD/jbrowse-components/issues/2708
        bpPerPx = self.bpPerPx  # Browser window width is unknown and default session cannot be used to figure it out in JB2 code so could be 200-2000+ pixels.
        track_types = {}
        with open(self.config_json_file, "r") as config_file:
            config_json = json.load(config_file)
        if self.config_json:
            config_json.update(self.config_json)

                    else:
                        logging.debug(
                            "style data for %s = %s"
                            % (tId, style_data)
                        )
                    if style_data.get('type', None) is None:
                        style_data["type"] = "LinearBasicDisplay"
                    if "displays" in track_conf:
                        disp = track_conf["displays"][0]["type"]
                        style_data["type"] = disp
                    if track_conf.get("displays", None):

                            "displays": [style_data],
                        }
                    )
            first = [x for x in self.ass_first_contigs if x[0] == gnome]
            drdict = {
                "reversed": False,
                "assemblyName": gnome,
            }
            if len(first) > 0:
                [gnome, refName, end] = first[0]
                drdict["refName"] = refName
                drdict["start"] = 0
                end = int(end)
                drdict["end"] = end
            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(",", ""))

                            % ddl
                        )
            view_json = {
                "type": "LinearGenomeView",
                "offsetPx": 0,
                "bpPerPx": bpPerPx,
                "minimized": False,
                "tracks": tracks_data
            }
            if drdict.get("refName", None):
                # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome

            trackfiles = track.findall("files/trackFile")
            if trackfiles:
                for x in trackfiles:
                    isBed = False
                    if x.attrib['ext'] == "bed":
                        isBed = True
                    track_conf["label"] = "%s_%d" % (
                        x.attrib["label"].replace(" ", "_").replace(",", "_").replace("/", "_"),
                        trackI,
                    )
                    trackI += 1
                    track_conf["useuri"] = x.attrib["useuri"]
                    if is_multi_bigwig: