def get_genome_assembly_files(self, species: dict, grch37=False) -> list:
"""
This method retrieve the genome assembly files for a specific specie object
:param grch37: if the GrCh37 genome assembly is desired enable to true
:param species: species to download the file.
:return:
"""
files = []
try:
if grch37:
species['assembly'] = 'GRCh37'
file_name = '{}.{}.dna_sm.toplevel.fa.gz'.format(species['name'][0].upper() + species['name'][1:],
species['assembly'])
file_url = '{}/release-{}/fasta/{}/dna/{}'.format(
self.get_default_parameters()[self.CONFIG_KEY_DATA_DOWNLOADER][self.CONFIG_KEY_ENSEMBL_FTP][
self.CONFIG_KEY_BASE_URL],
species['release'], species['name'], file_name)
if grch37:
file_url = '{}/grch37/release-{}/fasta/{}/dna/{}'.format(
self.get_default_parameters()[self.CONFIG_KEY_DATA_DOWNLOADER][self.CONFIG_KEY_ENSEMBL_FTP][
self.CONFIG_KEY_BASE_URL],
species['release'], species['name'], file_name)
files.append(
download_file(file_url, self.get_local_path_root_ensembl_repo() + '/' + file_name, self.get_logger()))
except KeyError:
print("No valid info is available species: ", species)
return files
def get_pep_files(self, species: dict, grch37=False) -> list:
"""
Get the peptide files for a specific species object.
:return: List of files names.
"""
files = []
try:
# TODO: Would be better to check by API the assembly version
if grch37:
species['assembly'] = 'GRCh37'
file_name = '{}.{}.pep.all.fa.gz'.format(species['name'][0].upper() + species['name'][1:],
species['assembly'])
file_url = '{}/release-{}/fasta/{}/pep/{}'.format(
self.get_default_parameters()[self.CONFIG_KEY_DATA_DOWNLOADER][self.CONFIG_KEY_ENSEMBL_FTP][
self.CONFIG_KEY_BASE_URL],
species['release'], species['name'], file_name)
if grch37:
file_url = '{}/grch37/release-{}/fasta/{}/pep/{}'.format(
self.get_default_parameters()[self.CONFIG_KEY_DATA_DOWNLOADER][self.CONFIG_KEY_ENSEMBL_FTP][
self.CONFIG_KEY_BASE_URL],
species['release'], species['name'], file_name)
files.append(
download_file(file_url, self.get_local_path_root_ensembl_repo() + '/' + file_name, self.get_logger()))
except KeyError:
print("No valid info is available species: ", species)
return files
def get_gtf_files(self, species: dict) -> list:
"""
This method retrieve the gtf files for a specific specie object
:param species:
:return:
"""
"""
Generate GTF file name from the species info and download the GTF file
"""
files = []
try:
file_name = '{}.{}.{}.gtf.gz'.format(
species['name'][0].upper() + species['name'][1:],
species['assembly'],
species['release'],
)
file_url = '{}/release-{}/gtf/{}/{}'.format(
self.get_default_parameters()[self.CONFIG_KEY_DATA_DOWNLOADER][
self.CONFIG_KEY_ENSEMBL_FTP][self.CONFIG_KEY_BASE_URL],
species['release'], species['name'], file_name)
files.append(
download_file(
file_url,
self.get_local_path_root_ensembl_repo() + '/' + file_name,
self.get_logger()))
except KeyError:
self.get_logger().debug("No valid info is available species: ",
species)
return files
def download_one_study(self, download_study):
file_name = '{}.tar.gz'.format(download_study)
file_url = '{}/{}'.format(
self.get_default_parameters()[self.CONFIG_KEY_DATA_DOWNLOADER][self.CONFIG_KEY_CBIOPORTAL_DOWNLOAD_URL],
file_name)
file_name = download_file(file_url, self.get_local_path_root_cbioportal_repo() + '/' + file_name, self.get_logger())
if file_name is not None:
msg = "The following study '{}' has been downloaded. ".format(download_study)
else:
msg = "The following study '{}' hasn't been downloaded. ".format(download_study)
self.get_logger().debug(msg)
return file_name
def get_vcf_files(self, species: dict) -> list:
"""
This method retrieve the vcf file for a specific specie object
:param species:
:return:
"""
files = []
try:
file_name = '{}_incl_consequences.vcf.gz'.format(species['name'])
file_url = '{}/release-{}/variation/vcf/{}/'.format(
self.get_default_parameters()[self.CONFIG_KEY_DATA_DOWNLOADER][self.CONFIG_KEY_ENSEMBL_FTP][
self.CONFIG_KEY_BASE_URL], species['release'], species['name'])
downloaded_file = download_file(file_url + file_name, self.get_local_path_root_ensembl_repo() + '/' + file_name,
self.get_logger())
if downloaded_file is not None:
files.append(downloaded_file)
elif species['name'] == 'homo_sapiens':
# for humans the variants are stored per chromosome, so we need to download them all and combine them into one file here"
chrN = 1
file_name = '{}_incl_consequences-chr{}.vcf.gz'.format(species['name'], chrN)
downloaded_file = download_file(file_url + file_name,
self.get_local_path_root_ensembl_repo() + '/' + file_name, self.get_logger())
if downloaded_file is not None:
# if chr1 is downloaded then try all others
files.append(downloaded_file)
for chrN in range(2, 23): # chr2-22
file_name = '{}_incl_consequences-chr{}.vcf.gz'.format(species['name'], chrN)
files.append(
download_file(file_url + file_name, self.get_local_path_root_ensembl_repo() + '/' + file_name,
self.get_logger()))
file_name = '{}_incl_consequences-chr{}.vcf.gz'.format(species['name'], 'X')
files.append(download_file(file_url + file_name, self.get_local_path_root_ensembl_repo() + '/' + file_name,
self.get_logger()))
file_name = '{}_incl_consequences-chr{}.vcf.gz'.format(species['name'], 'Y')
files.append(download_file(file_url + file_name, self.get_local_path_root_ensembl_repo() + '/' + file_name,
self.get_logger()))
file_name = '{}_incl_consequences-chr{}.vcf.gz'.format(species['name'], 'MT')
files.append(download_file(file_url + file_name, self.get_local_path_root_ensembl_repo() + '/' + file_name,
self.get_logger()))
except KeyError:
self.get_logger().debug("No valid info is available species: ", species)
return files
def get_ncrna_files(self, species: dict) -> list:
"""
Get the cds files for a specific species object.
:return: List of files names.
"""
files = []
try:
file_name = '{}.{}.ncrna.fa.gz'.format(
species['name'][0].upper() + species['name'][1:],
species['assembly'])
file_url = '{}/release-{}/fasta/{}/ncrna/{}'.format(
self.get_default_parameters()[self.CONFIG_KEY_DATA_DOWNLOADER][
self.CONFIG_KEY_ENSEMBL_FTP][self.CONFIG_KEY_BASE_URL],
species['release'], species['name'], file_name)
files.append(
download_file(
file_url,
self.get_local_path_root_ensembl_repo() + '/' + file_name,
self.get_logger()))
except KeyError:
print("No valid info is available species: ", species)
return files
