comparison jbrowse2.py @ 24:fb6cc7bc24df draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit cde4b8a574ded34a0ff8df3ecafc1a057787dcfb-dirty

23:39b717d934a8

                    genome_name  # first one for all tracks - other than paf
                )
                self.genome_firstcontig = None
                fl = open(fapath, "r").readline().strip().split(">", 1)
                if len(fl) > 1:
                    self.genome_firstcontig = fl[1].strip()
        if self.config_json.get("assemblies", None):
            self.config_json["assemblies"] += assemblies
        else:
            self.config_json["assemblies"] = assemblies

                self.add_hic(
                    dataset_path,
                    outputTrackConfig,
                )
            elif dataset_ext in ("cool", "mcool", "scool"):
                hictempd = tempfile.mkdtemp()
                hic_path = os.path.join(
                    self.outdir, "%s_%d_%s.hic" % (track_human_label, i, dataset_ext)
                )
                self.subprocess_check_call(
                    [
                        "hictk",
                        "convert",
                        "-f",
                        "--output-fmt",
                        "hic",
                        "--tmpdir",
                        hictempd,
                        dataset_path,
                        hic_path,
                    ]
                )
                self.add_hic(
                    hic_path,
                    outputTrackConfig,
                )
                shutil.rmtree(hictempd)
            elif dataset_ext in ("bed",):
                self.add_bed(
                    dataset_path,
                    dataset_ext,
                    outputTrackConfig,

            loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl)
            if loc_match:
                refName = loc_match.group(1)
                drdict["refName"] = refName
                if loc_match.group(2) > "":
                    drdict["start"] = int(loc_match.group(2))
                if loc_match.group(3) > "":
                    drdict["end"] = int(loc_match.group(3))
            else:
                logging.info(
                    "@@@ regexp could not match contig:start..end in the supplied location %s - please fix"
                    % ddl
                )

24:fb6cc7bc24df

                    genome_name  # first one for all tracks - other than paf
                )
                self.genome_firstcontig = None
                fl = open(fapath, "r").readline().strip().split(">", 1)
                if len(fl) > 1:
                    self.genome_firstcontig = fl[1].split().strip()
        if self.config_json.get("assemblies", None):
            self.config_json["assemblies"] += assemblies
        else:
            self.config_json["assemblies"] = assemblies

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

            loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl)
            if loc_match:
                refName = loc_match.group(1)
                drdict["refName"] = refName
                if loc_match.group(2) > "":
                    drdict["start"] = int(loc_match.group(2).replace(',',''))
                if loc_match.group(3) > "":
                    drdict["end"] = int(loc_match.group(3).replace(',',''))
            else:
                logging.info(
                    "@@@ regexp could not match contig:start..end in the supplied location %s - please fix"
                    % ddl
                )