def split(*items): """Split samples into all possible genomes for alignment. """ out = [] for data in [x[0] for x in items]: dis_orgs = data["config"]["algorithm"].get("disambiguate") if dis_orgs: if not data.get("disambiguate", None): data["disambiguate"] = { "genome_build": data["genome_build"], "base": True } out.append([data]) # handle the instance where a single organism is disambiguated if isinstance(dis_orgs, basestring): dis_orgs = [dis_orgs] for dis_org in dis_orgs: dis_data = copy.deepcopy(data) dis_data["disambiguate"] = {"genome_build": dis_org} dis_data["genome_build"] = dis_org dis_data = run_info.add_reference_resources(dis_data) out.append([dis_data]) else: out.append([data]) return out
def split(*items): """Split samples into all possible genomes for alignment. """ out = [] for data in [x[0] for x in items]: dis_orgs = data["config"]["algorithm"].get("disambiguate") if dis_orgs: data["disambiguate"] = {"genome_build": data["genome_build"], "base": True} out.append([data]) for dis_org in dis_orgs: dis_data = copy.deepcopy(data) dis_data["disambiguate"] = {"genome_build": dis_org} dis_data["genome_build"] = dis_org dis_data = run_info.add_reference_resources(dis_data) out.append([dis_data]) else: out.append([data]) return out
def split(items): """Split samples into all possible genomes for alignment. """ out = [] for data in [x[0] for x in items]: dis_orgs = data["config"]["algorithm"].get("disambiguate") if dis_orgs: data["disambiguate"] = { "genome_build": data["genome_build"], "base": True } out.append([data]) for dis_org in dis_orgs: dis_data = copy.deepcopy(data) dis_data["disambiguate"] = {"genome_build": dis_org} dis_data["genome_build"] = dis_org dis_data = run_info.add_reference_resources(dis_data) out.append([dis_data]) else: out.append([data]) return out
def split(*items): """Split samples into all possible genomes for alignment. """ out = [] for data in [x[0] for x in items]: dis_orgs = data["config"]["algorithm"].get("disambiguate") if dis_orgs: if not data.get("disambiguate", None): data["disambiguate"] = {"genome_build": data["genome_build"], "base": True} out.append([data]) # handle the instance where a single organism is disambiguated if isinstance(dis_orgs, basestring): dis_orgs = [dis_orgs] for dis_org in dis_orgs: dis_data = copy.deepcopy(data) dis_data["disambiguate"] = {"genome_build": dis_org} dis_data["genome_build"] = dis_org dis_data = run_info.add_reference_resources(dis_data) out.append([dis_data]) else: out.append([data]) return out
def config_without_disambiguate(self): config = self._get_base_config() config["genome_build"] = "hg19" config.update(self._get_filepaths()) config = run_info.add_reference_resources(config) return config