comparison jbrowse2.py @ 15:cce8dacb240f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty

14:7c2e28e144f3

from collections import defaultdict

logging.basicConfig(level=logging.INFO)
log = logging.getLogger("jbrowse")

JB2VER = "v2.10.0"
# version pinned for cloning

TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
GALAXY_INFRASTRUCTURE_URL = None
JB2REL = "v2.10.0"

            self.genome_names.append(genome_name)
            if self.genome_name is None:
                self.genome_name = (
                    genome_name  # first one for all tracks - other than paf
                )
            if self.config_json.get("assemblies", None):
                self.config_json["assemblies"] += assemblies
            else:
                self.config_json["assemblies"] = assemblies

    def make_assembly(self, fapath, gname):
        hashData = [
            fapath,
            gname,

        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)
        os.unlink(gff3)

    def add_bigwig(self, data, trackData):
        url = "%s.bigwig" % trackData["label"]
        # slashes in names cause path trouble
        dest = os.path.join(self.outdir, url)
        cmd = ["cp", data, dest]
        self.subprocess_check_call(cmd)

        }
        style_json = self._prepare_track_style(trackDict)
        trackDict["style"] = style_json
        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)
        logging.debug("#### wig trackData=%s" % str(trackData))

    def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs):
        tId = trackData["label"]
        fname = "%s.bam" % trackData["label"]
        dest = "%s/%s" % (self.outdir, fname)

    def add_paf(self, data, trackData, pafOpts, **kwargs):
        tname = trackData["name"]
        tId = trackData["label"]
        pgname = pafOpts["genome_label"]
        if len(pgname.split() > 1):
            pgname = pgname.split()[
                0
            ]  # trouble from spacey names in command lines avoidance
        asstrack, gname = self.make_assembly(pafOpts["genome"], pgname)
        self.genome_names.append(pgname)
        if self.config_json.get("assemblies", None):
            self.config_json["assemblies"].append(asstrack)
        else:
            self.config_json["assemblies"] = [
                asstrack,
            ]

        url = "%s.paf" % (trackData["label"])
        dest = "%s/%s" % (self.outdir, url)
        self.symlink_or_copy(os.path.realpath(data), dest)
        trackDict = {
            "type": "SyntenyTrack",

            "adapter": {
                "type": "PAFAdapter",
                "pafLocation": {"uri": url},
                "assemblyNames": [self.genome_name, pgname],
            },
        }
        style_json = self._prepare_track_style(trackDict)
        trackDict["style"] = style_json
        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)

                self.add_blastxml(
                    dataset_path, outputTrackConfig, track["conf"]["options"]["blast"]
                )
            elif dataset_ext == "vcf":
                self.add_vcf(dataset_path, outputTrackConfig)
            else:
                log.warn("Do not know how to handle %s", dataset_ext)
            # Return non-human label for use in other fields
            yield outputTrackConfig["label"]

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

                item.tag: parse_style_conf(item)
                for item in track.find("options/style_labels")
            }

        track_conf["conf"] = etree_to_dict(track.find("options"))
        keys = jc.process_annotations(track_conf)

        if keys:
            for key in keys:
                default_session_data["visibility"][

                    ]  # TODO do we need this anymore?
                if track_conf.get("style_lables", None):
                    default_session_data["style_labels"][key] = track_conf.get(
                        "style_labels", None
                    )

        default_session_data["defaultLocation"] = root.find(
            "metadata/general/defaultLocation"
        ).text
        default_session_data["session_name"] = root.find(
            "metadata/general/session_name"
        ).text

        general_data = {
            "analytics": root.find("metadata/general/analytics").text,
            "primary_color": root.find("metadata/general/primary_color").text,
            "secondary_color": root.find("metadata/general/secondary_color").text,
            "tertiary_color": root.find("metadata/general/tertiary_color").text,
            "quaternary_color": root.find("metadata/general/quaternary_color").text,
            "font_size": root.find("metadata/general/font_size").text,
        }
        track_conf["category"] = track.attrib["cat"]
        track_conf["format"] = track.attrib["format"]
        try:
            # Only pertains to gff3 + blastxml. TODO?
            track_conf["style"] = {t.tag: t.text for t in track.find("options/style")}
        except TypeError:
            track_conf["style"] = {}
            pass
        track_conf["conf"] = etree_to_dict(track.find("options"))
        jc.add_general_configuration(general_data)
    jc.config_json["tracks"] = jc.tracksToAdd
    jc.write_config()
    jc.add_default_session(default_session_data)

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

15:cce8dacb240f

from collections import defaultdict

logging.basicConfig(level=logging.INFO)
log = logging.getLogger("jbrowse")

JB2VER = "v2.10.1"
# version pinned for cloning

TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
GALAXY_INFRASTRUCTURE_URL = None
JB2REL = "v2.10.0"

            self.genome_names.append(genome_name)
            if self.genome_name is None:
                self.genome_name = (
                    genome_name  # first one for all tracks - other than paf
                )
        if self.config_json.get("assemblies", None):
            self.config_json["assemblies"] += assemblies
        else:
            self.config_json["assemblies"] = assemblies

    def make_assembly(self, fapath, gname):
        hashData = [
            fapath,
            gname,

        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)
        os.unlink(gff3)

    def add_bigwig(self, data, trackData):
        """ "type": "LinearWiggleDisplay",
        "configuration": {},
        "selectedRendering": "",
        "resolution": 1,
        "posColor": "rgb(228, 26, 28)",
        "negColor": "rgb(255, 255, 51)",
        "constraints": {}
        """
        url = "%s.bigwig" % trackData["label"]
        # slashes in names cause path trouble
        dest = os.path.join(self.outdir, url)
        cmd = ["cp", data, dest]
        self.subprocess_check_call(cmd)

        }
        style_json = self._prepare_track_style(trackDict)
        trackDict["style"] = style_json
        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)
        logging.info("#### wig trackData=%s" % str(trackData))

    def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs):
        tId = trackData["label"]
        fname = "%s.bam" % trackData["label"]
        dest = "%s/%s" % (self.outdir, fname)

    def add_paf(self, data, trackData, pafOpts, **kwargs):
        tname = trackData["name"]
        tId = trackData["label"]
        pgname = pafOpts["genome_label"]
        if len(pgname.split()) > 1:
            pgname = pgname.split()[
                0
            ]  # trouble from spacey names in command lines avoidance
        asstrack = self.make_assembly(pafOpts["genome"], pgname)
        self.genome_names.append(pgname)
        if self.config_json.get("assemblies", None):
            self.config_json["assemblies"].append(asstrack)
        else:
            self.config_json["assemblies"] = [
                asstrack,
            ]
        url = "%s.paf" % (trackData["label"])
        dest = "%s/%s" % (self.outdir, url)
        self.symlink_or_copy(os.path.realpath(data), dest)
        trackDict = {
            "type": "SyntenyTrack",

            "adapter": {
                "type": "PAFAdapter",
                "pafLocation": {"uri": url},
                "assemblyNames": [self.genome_name, pgname],
            },
            # "displays": [
                # {
                    # "type": "LinearSyntenyDisplay",
                    # "displayId": "%s-LinearSyntenyDisplay" % tId,
                # },
                # {
                    # "type": "DotPlotDisplay",
                    # "displayId": "%s-DotPlotDisplay" % tId,
                # },
            # ],
        }
        style_json = self._prepare_track_style(trackDict)
        trackDict["style"] = style_json
        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)

                self.add_blastxml(
                    dataset_path, outputTrackConfig, track["conf"]["options"]["blast"]
                )
            elif dataset_ext == "vcf":
                self.add_vcf(dataset_path, outputTrackConfig)
            elif dataset_ext == "paf":
                self.add_paf(
                    dataset_path, outputTrackConfig, track["conf"]["options"]["synteny"]
                )
            else:
                log.warn("Do not know how to handle %s", dataset_ext)
            # Return non-human label for use in other fields
            yield outputTrackConfig["label"]

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

                item.tag: parse_style_conf(item)
                for item in track.find("options/style_labels")
            }

        track_conf["conf"] = etree_to_dict(track.find("options"))
        track_conf["category"] = track.attrib["cat"]
        track_conf["format"] = track.attrib["format"]
        try:
            # Only pertains to gff3 + blastxml. TODO?
            track_conf["style"] = {t.tag: t.text for t in track.find("options/style")}
        except TypeError:
            track_conf["style"] = {}
            pass
        track_conf["conf"] = etree_to_dict(track.find("options"))
        keys = jc.process_annotations(track_conf)

        if keys:
            for key in keys:
                default_session_data["visibility"][

                    ]  # TODO do we need this anymore?
                if track_conf.get("style_lables", None):
                    default_session_data["style_labels"][key] = track_conf.get(
                        "style_labels", None
                    )
    default_session_data["defaultLocation"] = root.find(
        "metadata/general/defaultLocation"
    ).text
    default_session_data["session_name"] = root.find(
        "metadata/general/session_name"
    ).text
    general_data = {
        "analytics": root.find("metadata/general/analytics").text,
        "primary_color": root.find("metadata/general/primary_color").text,
        "secondary_color": root.find("metadata/general/secondary_color").text,
        "tertiary_color": root.find("metadata/general/tertiary_color").text,
        "quaternary_color": root.find("metadata/general/quaternary_color").text,
        "font_size": root.find("metadata/general/font_size").text,
    }
    jc.add_general_configuration(general_data)
    trackconf = jc.config_json.get("tracks", None)
    if trackconf:
        jc.config_json["tracks"].update(jc.tracksToAdd)
    else:
        jc.config_json["tracks"] = jc.tracksToAdd
    jc.write_config()
    jc.add_default_session(default_session_data)
    # jc.text_index() not sure what broke here.