comparison jbrowse2.py @ 5:efc64d8f4b72 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9

4:54396f0323f4

logging.basicConfig(level=logging.INFO)
log = logging.getLogger("jbrowse")
TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
GALAXY_INFRASTRUCTURE_URL = None
JB2REL="v2.10.0"
# version pinned for cloning

mapped_chars = {
    ">": "__gt__",
    "<": "__lt__",

        style_data = {
            "type": "LinearBasicDisplay",
            "displayId": "%s-LinearBasicDisplay" % trackDict["trackId"],
        }

        if trackDict.get("displays", None):
            style_data["type"] = trackDict["displays"]["type"]
            style_data["displayId"] = trackDict["displays"]["displayId"]
        return {"displays": [style_data]}

    def process_genomes(self):
        assemblies = []
        for i, genome_node in enumerate(self.genome_paths):
            if self.debug:
                log.info("genome_node=%s" % str(genome_node))
            genome_name = genome_node["meta"]["dataset_dname"].strip()
            if len(genome_name.split()) > 1:
                genome_name = genome_name.split()[0]
                # spaces and cruft break scripts when substituted
            fapath = genome_node["path"]

            uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.fai',
            gziLocation:
            uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.gzi',
        Cool will not be likely to be a good fit - see discussion at https://github.com/GMOD/jbrowse-components/issues/2438
        """
        log.info("#### trackData=%s" % trackData)
        tId = trackData["label"]
        # can be served - if public.
        # dsId = trackData["metadata"]["dataset_id"]
        # url = "%s/api/datasets/%s/display?to_ext=hic " % (self.giURL, dsId)
        hname = trackData["name"]

                    "type": "LinearHicDisplay",
                    "displayId": "%s-LinearHicDisplay" % tId,
                },
            ],
        }
        # style_json = self._prepare_track_style(trackDict)
        # trackDict["style"] = style_json
        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)

    def add_maf(self, data, trackData):
        """

            gname,
            INSTALLED_TO,
            dest,
        ]
        self.subprocess_check_call(cmd)
        if True or self.debug:
            log.info("### convertMAF.sh called as %s" % " ".join(cmd))
        # Construct samples list
        # We could get this from galaxy metadata, not sure how easily.
        ps = subprocess.Popen(["grep", "^s [^ ]*", "-o", data], stdout=subprocess.PIPE)
        output = subprocess.check_output(("sort", "-u"), stdin=ps.stdout)
        ps.wait()
        outp = output.decode("ascii")
        soutp = outp.split("\n")
        samp = [x.split("s ")[1] for x in soutp if x.startswith("s ")]
        samples = [x.split(".")[0] for x in samp]
        if self.debug:
            log.info("### got samples = %s " % (samples))
        trackDict = {
            "type": "MafTrack",
            "trackId": tId,
            "name": trackData["name"],
            "adapter": {

                        "uri": fname + ".sorted.bed.gz.tbi",
                    },
                },
            },
            "assemblyNames": [self.genome_name],
        }
        # style_json = self._prepare_track_style(trackDict)
        # trackDict["style"] = style_json
        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)
        if self.config_json.get("plugins", None):
            self.config_json["plugins"].append(mafPlugin[0])
        else:

                    "displayId": "%s-LinearBasicDisplay" % tId,
                },
                {"type": "LinearArcDisplay", "displayId": "%s-LinearArcDisplay" % tId},
            ],
        }
        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)

        os.unlink(gff3)

                    "type": "LinearWiggleDisplay",
                    "displayId": "%s-LinearWiggleDisplay" % tId,
                }
            ],
        }
        # style_json = self._prepare_track_style(trackDict)
        # trackDict["style"] = style_json
        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)

    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)
        url = fname
        self.subprocess_check_call(["cp", data, dest])
        log.info("### copied %s to %s" % (data, dest))
        bloc = {"uri": url}
        if bam_index is not None and os.path.exists(os.path.realpath(bam_index)):
            # bai most probably made by galaxy and stored in galaxy dirs, need to copy it to dest
            self.subprocess_check_call(
                ["cp", os.path.realpath(bam_index), dest + ".bai"]

                    "type": "LinearAlignmentsDisplay",
                    "displayId": "%s-LinearAlignmentsDisplay" % tId,
                },
            ],
        }
        # style_json = self._prepare_track_style(trackDict)
        # trackDict["style"] = style_json
        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)

    def add_vcf(self, data, trackData):
        tId = trackData["label"]

                    "type": "LinearPairedArcDisplay",
                    "displayId": "%s-LinearPairedArcDisplay" % tId,
                },
            ],
        }
        # style_json = self._prepare_track_style(trackDict)
        # trackDict["style"] = style_json
        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)

    def _sort_gff(self, data, dest):
        # Only index if not already done

                    "displayId": "%s-LinearBasicDisplay" % tId,
                },
                {"type": "LinearArcDisplay", "displayId": "%s-LinearArcDisplay" % tId},
            ],
        }
        # style_json = self._prepare_track_style(trackDict)
        # trackDict["style"] = style_json
        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)

    def add_bed(self, data, ext, trackData):
        url = "%s.%s" % (trackData["label"], ext)

                    }
                },
            },
            "displays": [
                {
                    "type": "LinearBasicDisplay",
                    "displayId": "%s-LinearBasicDisplay" % tId,
                },
                {"type": "LinearArcDisplay", "displayId": "%s-LinearArcDisplay" % tId},
            ],
        }
        # style_json = self._prepare_track_style(trackDict)
        # trackDict["style"] = style_json
        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)

    def add_paf(self, data, trackData, pafOpts, **kwargs):
        tname = trackData["name"]

        # TODO using the default session for now, but check out session specs in the future https://github.com/GMOD/jbrowse-components/issues/2708

        # We need to know the track type from the config.json generated just before
        track_types = {}
        logging.info("### add default session has data = %s\n" % str(data))
        with open(self.config_json_file, "r") as config_file:
            config_json = json.load(config_file)
        logging.info("### config.json read \n%s\n" % (config_json))

        for track_conf in self.tracksToAdd:  # config_json["tracks"]:
            track_types[track_conf["trackId"]] = track_conf["type"]
        logging.info(
            "### self.tracksToAdd = %s; track_types = %s"
            % (str(self.tracksToAdd), str(track_types))
        )

        for on_track in data["visibility"]["default_on"]:
            style_data = {"type": "LinearBasicDisplay", "height": 100}
            if on_track in data["style"]:
                if "display" in data["style"][on_track]:

            json.dump(config_json, config_file, indent=2)

    def clone_jbrowse(self):
        """Clone a JBrowse directory into a destination directory."""
        dest = self.outdir
        cmd = ["jbrowse", "create", "-t",JB2REL, "-f", dest]
        self.subprocess_check_call(cmd)
        for fn in [
            "asset-manifest.json",
            "favicon.ico",
            "robots.txt",

        except TypeError:
            track_conf["style"] = {}
            pass
        track_conf["conf"] = etree_to_dict(track.find("options"))
        jc.add_general_configuration(general_data)
        print("## processed", str(track_conf), "trackIdlist", jc.trackIdlist)
    x = open(args.xml, "r").read()
    log.info(
        "###done processing xml=%s; trackIdlist=%s, config=%s"
        % (x, jc.trackIdlist, str(jc.config_json))
    )
    jc.config_json["tracks"] = jc.tracksToAdd
    if jc.usejson:
        jc.write_config()
    # jc.add_default_view()
    jc.add_default_session(default_session_data)

5:efc64d8f4b72

logging.basicConfig(level=logging.INFO)
log = logging.getLogger("jbrowse")
TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
GALAXY_INFRASTRUCTURE_URL = None
JB2REL = "v2.10.0"
# version pinned for cloning

mapped_chars = {
    ">": "__gt__",
    "<": "__lt__",

        style_data = {
            "type": "LinearBasicDisplay",
            "displayId": "%s-LinearBasicDisplay" % trackDict["trackId"],
        }

        if trackDict.get("displays", None):  # use first if multiple like bed
            style_data["type"] = trackDict["displays"][0]["type"]
            style_data["displayId"] = trackDict["displays"][0]["displayId"]
        return {
            "displays": [
                style_data,
            ]
        }

    def process_genomes(self):
        assemblies = []
        for i, genome_node in enumerate(self.genome_paths):
            genome_name = genome_node["meta"]["dataset_dname"].strip()
            if len(genome_name.split()) > 1:
                genome_name = genome_name.split()[0]
                # spaces and cruft break scripts when substituted
            fapath = genome_node["path"]

            uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.fai',
            gziLocation:
            uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.gzi',
        Cool will not be likely to be a good fit - see discussion at https://github.com/GMOD/jbrowse-components/issues/2438
        """
        tId = trackData["label"]
        # can be served - if public.
        # dsId = trackData["metadata"]["dataset_id"]
        # url = "%s/api/datasets/%s/display?to_ext=hic " % (self.giURL, dsId)
        hname = trackData["name"]

                    "type": "LinearHicDisplay",
                    "displayId": "%s-LinearHicDisplay" % tId,
                },
            ],
        }
        style_json = self._prepare_track_style(trackDict)
        trackDict["style"] = style_json
        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)

    def add_maf(self, data, trackData):
        """

            gname,
            INSTALLED_TO,
            dest,
        ]
        self.subprocess_check_call(cmd)
        # Construct samples list
        # We could get this from galaxy metadata, not sure how easily.
        ps = subprocess.Popen(["grep", "^s [^ ]*", "-o", data], stdout=subprocess.PIPE)
        output = subprocess.check_output(("sort", "-u"), stdin=ps.stdout)
        ps.wait()
        outp = output.decode("ascii")
        soutp = outp.split("\n")
        samp = [x.split("s ")[1] for x in soutp if x.startswith("s ")]
        samples = [x.split(".")[0] for x in samp]
        trackDict = {
            "type": "MafTrack",
            "trackId": tId,
            "name": trackData["name"],
            "adapter": {

                        "uri": fname + ".sorted.bed.gz.tbi",
                    },
                },
            },
            "assemblyNames": [self.genome_name],
            "displays": [
                {
                    "type": "LinearBasicDisplay",
                    "displayId": "%s-LinearBasicDisplay" % tId,
                },
                {"type": "LinearArcDisplay", "displayId": "%s-LinearArcDisplay" % tId},
            ],
        }
        style_json = self._prepare_track_style(trackDict)
        trackDict["style"] = style_json
        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)
        if self.config_json.get("plugins", None):
            self.config_json["plugins"].append(mafPlugin[0])
        else:

                    "displayId": "%s-LinearBasicDisplay" % tId,
                },
                {"type": "LinearArcDisplay", "displayId": "%s-LinearArcDisplay" % tId},
            ],
        }
        style_json = self._prepare_track_style(trackDict)
        trackDict["style"] = style_json
        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)

        os.unlink(gff3)

                    "type": "LinearWiggleDisplay",
                    "displayId": "%s-LinearWiggleDisplay" % tId,
                }
            ],
        }
        style_json = self._prepare_track_style(trackDict)
        trackDict["style"] = style_json
        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)

    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)
        url = fname
        self.subprocess_check_call(["cp", data, dest])
        bloc = {"uri": url}
        if bam_index is not None and os.path.exists(os.path.realpath(bam_index)):
            # bai most probably made by galaxy and stored in galaxy dirs, need to copy it to dest
            self.subprocess_check_call(
                ["cp", os.path.realpath(bam_index), dest + ".bai"]

                    "type": "LinearAlignmentsDisplay",
                    "displayId": "%s-LinearAlignmentsDisplay" % tId,
                },
            ],
        }
        style_json = self._prepare_track_style(trackDict)
        trackDict["style"] = style_json
        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)

    def add_vcf(self, data, trackData):
        tId = trackData["label"]

                    "type": "LinearPairedArcDisplay",
                    "displayId": "%s-LinearPairedArcDisplay" % tId,
                },
            ],
        }
        style_json = self._prepare_track_style(trackDict)
        trackDict["style"] = style_json
        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)

    def _sort_gff(self, data, dest):
        # Only index if not already done

                    "displayId": "%s-LinearBasicDisplay" % tId,
                },
                {"type": "LinearArcDisplay", "displayId": "%s-LinearArcDisplay" % tId},
            ],
        }
        style_json = self._prepare_track_style(trackDict)
        trackDict["style"] = style_json
        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)

    def add_bed(self, data, ext, trackData):
        url = "%s.%s" % (trackData["label"], ext)

                    }
                },
            },
            "displays": [
                {
                    "type": "LinearPileupDisplay",
                    "displayId": "%s-LinearPileupDisplay" % tId,
                },
                {
                    "type": "LinearBasicDisplay",
                    "displayId": "%s-LinearBasicDisplay" % tId,
                },
                {"type": "LinearArcDisplay", "displayId": "%s-LinearArcDisplay" % tId},
            ],
        }
        style_json = self._prepare_track_style(trackDict)
        trackDict["style"] = style_json
        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)

    def add_paf(self, data, trackData, pafOpts, **kwargs):
        tname = trackData["name"]

        # TODO using the default session for now, but check out session specs in the future https://github.com/GMOD/jbrowse-components/issues/2708

        # We need to know the track type from the config.json generated just before
        track_types = {}
        with open(self.config_json_file, "r") as config_file:
            config_json = json.load(config_file)

        for track_conf in self.tracksToAdd:  # config_json["tracks"]:
            track_types[track_conf["trackId"]] = track_conf["type"]

        for on_track in data["visibility"]["default_on"]:
            style_data = {"type": "LinearBasicDisplay", "height": 100}
            if on_track in data["style"]:
                if "display" in data["style"][on_track]:

            json.dump(config_json, config_file, indent=2)

    def clone_jbrowse(self):
        """Clone a JBrowse directory into a destination directory."""
        dest = self.outdir
        cmd = ["jbrowse", "create", "-t", JB2REL, "-f", dest]
        self.subprocess_check_call(cmd)
        for fn in [
            "asset-manifest.json",
            "favicon.ico",
            "robots.txt",

        except TypeError:
            track_conf["style"] = {}
            pass
        track_conf["conf"] = etree_to_dict(track.find("options"))
        jc.add_general_configuration(general_data)
    x = open(args.xml, "r").read()
    jc.config_json["tracks"] = jc.tracksToAdd
    if jc.usejson:
        jc.write_config()
    # jc.add_default_view()
    jc.add_default_session(default_session_data)