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
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
