def _upgrade_snpeff_data(galaxy_dir, args, remotes): """Install or upgrade snpEff databases, localized to reference directory. """ snpeff_version = effects.snpeff_version(args) if not snpeff_version: return for dbkey, ref_file in genome.get_builds(galaxy_dir): resource_file = os.path.join(os.path.dirname(ref_file), "%s-resources.yaml" % dbkey) if os.path.exists(resource_file): with open(resource_file) as in_handle: resources = yaml.load(in_handle) snpeff_db, snpeff_base_dir = effects.get_db({"genome_resources": resources, "reference": {"fasta": {"base": ref_file}}}) if snpeff_db: snpeff_db_dir = os.path.join(snpeff_base_dir, snpeff_db) if os.path.exists(snpeff_db_dir) and _is_old_database(snpeff_db_dir, args): shutil.rmtree(snpeff_db_dir) if not os.path.exists(snpeff_db_dir): print("Installing snpEff database %s in %s" % (snpeff_db, snpeff_base_dir)) dl_url = remotes["snpeff_dl_url"].format( snpeff_ver=snpeff_version.replace(".", "_"), genome=snpeff_db) dl_file = os.path.basename(dl_url) with utils.chdir(snpeff_base_dir): subprocess.check_call(["wget", "-c", "-O", dl_file, dl_url]) subprocess.check_call(["unzip", dl_file]) os.remove(dl_file) dl_dir = os.path.join(snpeff_base_dir, "data", snpeff_db) shutil.move(dl_dir, snpeff_db_dir) os.rmdir(os.path.join(snpeff_base_dir, "data"))
def _upgrade_snpeff_data(galaxy_dir, args, remotes): """Install or upgrade snpEff databases, localized to reference directory. """ snpeff_version = effects.snpeff_version(args) if not snpeff_version: return for dbkey, ref_file in genome.get_builds(galaxy_dir): resource_file = os.path.join(os.path.dirname(ref_file), "%s-resources.yaml" % dbkey) if os.path.exists(resource_file): with open(resource_file) as in_handle: resources = yaml.load(in_handle) snpeff_db, snpeff_base_dir = effects.get_db({"genome_resources": resources, "reference": {"fasta": {"base": ref_file}}}) if snpeff_db: snpeff_db_dir = os.path.join(snpeff_base_dir, snpeff_db) if os.path.exists(snpeff_db_dir) and _is_old_database(snpeff_db_dir, args): shutil.rmtree(snpeff_db_dir) if not os.path.exists(snpeff_db_dir): print("Installing snpEff database %s in %s" % (snpeff_db, snpeff_base_dir)) dl_url = remotes["snpeff_dl_url"].format( snpeff_ver=snpeff_version.replace(".", "_"), genome=snpeff_db) dl_file = os.path.basename(dl_url) with utils.chdir(snpeff_base_dir): subprocess.check_call(["wget", "--no-check-certificate", "-c", "-O", dl_file, dl_url]) subprocess.check_call(["unzip", dl_file]) os.remove(dl_file) dl_dir = os.path.join(snpeff_base_dir, "data", snpeff_db) shutil.move(dl_dir, snpeff_db_dir) os.rmdir(os.path.join(snpeff_base_dir, "data"))
def _is_old_database(db_dir, args): """Check for old database versions, supported in snpEff 4.1. """ snpeff_version = effects.snpeff_version(args) if LooseVersion(snpeff_version) >= LooseVersion("4.1"): pred_file = os.path.join(db_dir, "snpEffectPredictor.bin") if not utils.file_exists(pred_file): return True with gzip.open(pred_file) as in_handle: version_info = in_handle.readline().strip().split("\t") program, version = version_info[:2] if not program.lower() == "snpeff" or LooseVersion(snpeff_version) > LooseVersion(version): return True return False