def get_gi_map(self, gi_map):
'''download gi_taxid_prot.dmp.gz from ncbi server and extract the complete file'''
local_version = self.DOWNLOAD_FOLDER + os.sep + gi_map
# test for actual or existing file
if not os.path.exists(local_version) or not self.is_actual(self.DOWNLOAD_FOLDER, gi_map):
try:
sys.stdout.write("Download %s from %s ...\n" % (gi_map, self.FTP_SERVER))
# download file
f = open(local_version, "wb")
self.get_connection().retrbinary("RETR " + gi_map, f.write)
f.close()
except:
raise FtpDownloadException(gi_map)
else:
ActualException(gi_map)
# extract file, if no extracted content exists
if not os.path.exists(str.strip(local_version, '.gz')):
extract_gz(local_version, self.DOWNLOAD_FOLDER)
return os.path.abspath(str.strip(local_version, '.gz'))
def download_file(self, local_folder, item):
'''download and extract a single file from ftp source'''
# specify save location
local_file = local_folder + os.sep + item
try:
# open local file stream
f = open(local_file, "wb")
# copy remote stream to local stream
self.get_connection().retrbinary("RETR " + item, f.write)
f.close()
except:
raise FtpDownloadException(item)
# check endings of files for typical compressing endings
if is_compressed(local_file):
# extract *.tgz files
if is_tgz(local_file):
extract_tar(local_file, local_folder)
# unpack gunzip files and ignore *.tar.gz (because of metacv db creation)
elif is_gz(local_file):
extract_gz(local_file)
else:
pass
def get_idmapping(self, idmapping):
'''download idmapping.dat.gz from uniprot server and extract the complete file'''
local_idmapping = self.DOWNLOAD_FOLDER + os.sep + idmapping
# test for actual or existing file
if not os.path.exists(local_idmapping) or not self.is_actual(self.DOWNLOAD_FOLDER, idmapping):
try:
sys.stdout.write("Download %s from %s ...\n" % (idmapping, self.FTP_SERVER))
# download file
f = open(local_idmapping, "wb")
self.get_connection().retrbinary("RETR " + idmapping, f.write)
f.close()
except:
raise FtpDownloadException(idmapping)
else:
ActualException(idmapping)
# extract file, if no extracted content exists
if not os.path.exists(str.strip(local_idmapping, '.gz')):
try:
extract_gz(local_idmapping, self.DOWNLOAD_FOLDER)
except:
raise ExtractionException(idmapping)
return os.path.abspath(str.strip(local_idmapping, '.gz'))