comparison jbrowse2.py @ 29:f728cf0df71d draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit fe89199bded3f50aefb6958f0c4e85eede77ad81-dirty

28:9a5c409f33f4

        """
        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"]
        dest = os.path.join(self.outdir, hname)
        cmd = ["cp", data, dest]
        # these can be very big.
        self.subprocess_check_call(cmd)
        floc = {
            "uri": hname,
        }
        trackDict = {
            "type": "HicTrack",

        }
        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)

                self.add_hic(
                    dataset_path,
                    outputTrackConfig,
                )
            elif dataset_ext in ("cool", "mcool", "scool"):
                hic_path = os.path.join(
                    self.outdir, "%s_%d_%s.hic" % (track_human_label, i, dataset_ext)
                )
                self.subprocess_check_call(
                    [
                        "hictk",
                        "convert",
                        "-f",

                        "hic",
                        dataset_path,
                        hic_path,
                    ]
                )
                self.add_hic(
                    hic_path,
                    outputTrackConfig,
                )
            elif dataset_ext in ("bed",):

                    dataset_path,
                    outputTrackConfig,
                    track["conf"]["options"]["paf"],
                )
            else:
                log.warn("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, data):
        """

            else:
                logging.info(
                    "@@@ regexp could not match contig:start..end in the supplied location %s - please fix"
                    % ddl
                )

        if drdict.get("refName", None):
            # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome
            view_json["displayedRegions"] = [
                drdict,
            ]

29:f728cf0df71d

        """
        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["hic_url"]
        floc = {
            "uri": hname,
        }
        trackDict = {
            "type": "HicTrack",

        }
        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)

                self.add_hic(
                    dataset_path,
                    outputTrackConfig,
                )
            elif dataset_ext in ("cool", "mcool", "scool"):
                hic_url = "%s_%d.hic" % (track_human_label, i)
                hic_path = os.path.join(self.outdir, hic_url)
                self.subprocess_check_call(
                    [
                        "hictk",
                        "convert",
                        "-f",

                        "hic",
                        dataset_path,
                        hic_path,
                    ]
                )
                outputTrackConfig["hic_url"] = hic_url
                self.add_hic(
                    hic_path,
                    outputTrackConfig,
                )
            elif dataset_ext in ("bed",):

                    dataset_path,
                    outputTrackConfig,
                    track["conf"]["options"]["paf"],
                )
            else:
                logging.warn("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, data):
        """

            else:
                logging.info(
                    "@@@ regexp could not match contig:start..end in the supplied location %s - please fix"
                    % ddl
                )
        else:
            drdict["refName"] = self.genome_firstcontig
        if drdict.get("refName", None):
            # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome
            view_json["displayedRegions"] = [
                drdict,
            ]