comparison jbrowse2.py @ 72:2bdb748df098 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 9d5e563dde653450723415b0fccd2ebb4b82477e

71:e26a8a6d2d2e

        self.trackIdlist.append(tId)

    def add_paf(self, data, trackData, pafOpts, **kwargs):
        tname = trackData["name"]
        tId = trackData["label"]
        categ = trackData["category"]
        pgnames = [
            x.strip() for x in pafOpts["genome_label"].split(",") if len(x.strip()) > 0
        ]
        pgpaths = [

        logging.debug(
            "### add_paf got pafOpts=%s, pgnames=%s, pgpaths=%s for %s"
            % (pafOpts, pgnames, pgpaths, tId)
        )
        for i, gname in enumerate(pgnames):
            lab = trackData["label"]
            if len(gname.split()) > 1:
                gname = gname.split()[0]
            passnames.append(gname)
            # trouble from spacey names in command lines avoidance
            useuri = pgpaths[i].startswith("http://") or pgpaths[i].startswith(
                "https://"
            )
            if not useuri:
                url = "%s.paf" % (lab)
            else:
                url = data
            if gname not in self.genome_names:
                # ignore if already there - eg for duplicates among pafs.
                asstrack = self.make_assembly(pgpaths[i], gname, useuri)
                self.genome_names.append(gname)
                self.tracksToAdd[gname] = []
                self.assemblies.append(asstrack)
                if not useuri:
                    dest = "%s/%s" % (self.outdir, url)
                    self.symlink_or_copy(os.path.realpath(data), dest)
        trackDict = {
            "type": "SyntenyTrack",
            "trackId": tId,
            "assemblyNames": passnames,
            "category": [

                "assemblyNames": passnames,
            },
            "displays": [
                {
                    "type": "LGVSyntenyDisplay",
                    "displayId": "%s-LGVSyntenyDisplay" % lab,
                },
                {"type": "DotplotDisplay", "displayId": "%s-DotplotDisplay" % lab},
                {
                    "type": "LinearComparativeDisplay",
                    "displayId": "%s-LinearComparativeDisplay" % lab,
                },
                {
                    "type": "LinearSyntenyDisplay",
                    "displayId": "%s-LinearSyntenyDisplay" % lab,
                },
            ],
        }
        style_json = {
            "displays": [
                {
                    "type": "LGVSyntenyDisplay",
                    "displayId": "%s-LGVSyntenyDisplay" % lab,
                }
            ]
        }
        trackDict["style"] = style_json
        self.tracksToAdd[trackData["assemblyNames"]].append(trackDict)

                view_json = {"type": "LinearGenomeView", "tracks": tracks_data}
                refName = self.assmeta[gnome][0].get("genome_firstcontig", None)
                drdict = {
                    "reversed": False,
                    "assemblyName": gnome,
                    "start": 1,
                    "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 "views" not in session_json:
            session_json["views"] = session_views
        else:
            session_json["views"] += session_views

        config_json["defaultSession"] = session_json
        self.config_json.update(config_json)

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

    def add_general_configuration(self, data):
        """

72:2bdb748df098

        self.trackIdlist.append(tId)

    def add_paf(self, data, trackData, pafOpts, **kwargs):
        tname = trackData["name"]
        tId = trackData["label"]
        url = "%s.paf" % tId
        useuri = data.startswith("http://") or data.startswith("https://")
        if not useuri:
            dest = "%s/%s" % (self.outdir, url)
            self.symlink_or_copy(os.path.realpath(data), dest)
        else:
            url = data
        categ = trackData["category"]
        pgnames = [
            x.strip() for x in pafOpts["genome_label"].split(",") if len(x.strip()) > 0
        ]
        pgpaths = [

        logging.debug(
            "### add_paf got pafOpts=%s, pgnames=%s, pgpaths=%s for %s"
            % (pafOpts, pgnames, pgpaths, tId)
        )
        for i, gname in enumerate(pgnames):
            if len(gname.split()) > 1:
                gname = gname.split()[0]
            passnames.append(gname)
            # trouble from spacey names in command lines avoidance
            useuri = pgpaths[i].startswith("http://") or pgpaths[i].startswith(
                "https://"
            )

            if gname not in self.genome_names:
                # ignore if already there - eg for duplicates among pafs.
                asstrack = self.make_assembly(pgpaths[i], gname, useuri)
                self.genome_names.append(gname)
                self.tracksToAdd[gname] = []
                self.assemblies.append(asstrack)
        trackDict = {
            "type": "SyntenyTrack",
            "trackId": tId,
            "assemblyNames": passnames,
            "category": [

                "assemblyNames": passnames,
            },
            "displays": [
                {
                    "type": "LGVSyntenyDisplay",
                    "displayId": "%s-LGVSyntenyDisplay" % tId,
                },
                {
                    "type": "DotplotDisplay",
                    "displayId": "%s-DotplotDisplay" % tId,
                },
                {
                    "type": "LinearComparativeDisplay",
                    "displayId": "%s-LinearComparativeDisplay" % tId,
                },
                {
                    "type": "LinearSyntenyDisplay",
                    "displayId": "%s-LinearSyntenyDisplay" % tId,
                },
            ],
        }
        style_json = {
            "displays": [
                {
                    "type": "LGVSyntenyDisplay",
                    "displayId": "%s-LGVSyntenyDisplay" % tId,
                }
            ]
        }
        trackDict["style"] = style_json
        self.tracksToAdd[trackData["assemblyNames"]].append(trackDict)

                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 "views" not in session_json:
            session_json["views"] = session_views
        else:
            session_json["views"] += session_views
        pp = json.dumps(session_views, indent=2)
        config_json["defaultSession"] = session_json
        self.config_json.update(config_json)
        logging.debug("defaultSession=%s" % (pp))
        with open(self.config_json_file, "w") as config_file:
            json.dump(self.config_json, config_file, indent=2)

    def add_general_configuration(self, data):
        """