comparison jbrowse2.py @ 27:4ff1ed2065cc draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit d733fb18a02929c9e9959ad30bd0f1368118e924-dirty

26:e578621acb13

                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"]

        }

        if data.get("defaultLocation", ""):
            ddl = data["defaultLocation"]
            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(',',''))

            else:
                logging.info(
                    "@@@ regexp could not match contig:start..end in the supplied location %s - please fix"
                    % ddl
                )
        elif self.genome_firstcontig is not None:
            drdict["refName"] = self.genome_firstcontig
            logging.info(
                "@@@ no defaultlocation found for default session - using %s as first contig found"
                % 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,

27:4ff1ed2065cc

                self.add_vcf(dataset_path, outputTrackConfig)
            elif dataset_ext == "paf":
                self.add_paf(
                    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"]

        }

        if data.get("defaultLocation", ""):
            ddl = data["defaultLocation"]
            loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl)
            # allow commas like 100,000 but ignore as integer
            if loc_match:
                refName = loc_match.group(1)
                drdict["refName"] = refName
                if loc_match.group(2) > "":
                    drdict["start"] = int(loc_match.group(2).replace(',',''))

            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,