def download_gaf(name):
"""
Download gaf file
"""
dest = get_fname(name)
url = const.ASSOCIATION_MAP.get(name)
utils.download(url=url, dest_name=dest)
return
def download_prebuilt():
"""
Downloads prebuild databases.
"""
url = "http://data.biostarhandbook.com/bio/"
url_sqlite = f"{url}/taxdb.sqlite"
url_json = f"{url}/taxdb.json"
utils.download(url=url_sqlite, dest_name=SQLITE_DB_NAME, cache=True)
utils.download(url=url_json, dest_name=JSON_DB_NAME, cache=True)
def fetch_genbank(acc, dest_name):
"""
Returns a genbank file.
"""
try:
db = 'nuccore'
rettype, retmode = "gbwithparts", "text"
params = dict(db=db, rettype=rettype, id=acc, retmode=retmode)
utils.download(EFETCH_URL, params=params, dest_name=dest_name)
except Exception as exc:
utils.error(exc)
def download_file(url, dest):
# Split the urls
(scheme, loc, path, query, frag) = urlsplit(url)
# Last member of the path is the prefix for each file.
prefix = path.split("/")[-1]
# Remote file name.
file_name = f"{prefix}_genomic.gbff.gz"
# Remote file path.
file_path = f"{path}/{file_name}"
# Genbank url.
file_url = urlunsplit((scheme, loc, file_path, '', ''))
# Download the file.
utils.download(url=file_url, dest_name=dest)
return
def update_taxdump(url=TAXDB_URL, dest_name=TAXDB_NAME):
"""
Downloads taxdump file.
"""
utils.download(url=url, dest_name=dest_name)
def download_assembly(url=ASSEMBLY_URL, dest_name=ASSEMBLY_FILE_NAME):
"""
Downloads the assembly data.
"""
utils.download(url=url, dest_name=dest_name)
def download_terms():
utils.download(url=GO_URL, dest_name=GO_FILE)
utils.download(url=SO_URL, dest_name=SO_FILE)
return