def test_index_ensembl_files(self):
"""Test the instantiation of some files for creating a datasource file."""
output_dir = "out/"
GenomeBuildInstallUtils.create_ensembl_transcript_datasource(ensembl_species="saccharomyces_cerevisiae", genome_build="sacCer3")
self.assertTrue(os.path.exists(output_dir + "ensembl/sacCer3"))
self.assertTrue(os.path.exists(output_dir + "ensembl/ensembl.config"))
statinfo = os.stat(output_dir + "ensembl/ensembl.config")
self.assertTrue(statinfo.st_size > 0, "generated config file (" + output_dir + "ensembl/ensembl.config) is empty.")
def test_index_ensembl_files(self):
"""Test the instantiation of some files for creating a datasource file."""
output_dir = "out/"
GenomeBuildInstallUtils.create_ensembl_transcript_datasource(
ensembl_species="saccharomyces_cerevisiae", genome_build="sacCer3")
self.assertTrue(os.path.exists(output_dir + "ensembl/sacCer3"))
self.assertTrue(os.path.exists(output_dir + "ensembl/ensembl.config"))
statinfo = os.stat(output_dir + "ensembl/ensembl.config")
self.assertTrue(
statinfo.st_size > 0, "generated config file (" + output_dir +
"ensembl/ensembl.config) is empty.")
def test_previous_release_download(self):
"""Download an older ensembl transcript package. This test needs an internet connection and will fail w/o one.
"""
download_dir = "out/test_ensembl_download_previous/"
release_num = "68"
MutUtils.removeDir(download_dir)
os.mkdir(download_dir)
GenomeBuildInstallUtils.download_reference_data_from_ensembl(download_dir, "saccharomyces_cerevisiae", release=release_num)
downloaded_files = os.listdir(download_dir)
transcript_file = None
for f in downloaded_files:
if f.find("." + release_num + ".cdna.") != -1:
transcript_file = f
break
self.assertIsNotNone(transcript_file)
statinfo = os.stat(download_dir + transcript_file)
self.assertTrue(statinfo.st_size > 0, "downloaded transcript file (" + transcript_file + ") is empty.")
def test_current_download(self):
"""Download a current ensembl transcript package. This test needs an internet connection and can be slow."""
#ftp://ftp.ensembl.org/pub/release-71/fasta/saccharomyces_cerevisiae/cdna/
download_dir = "out/test_ensembl_download/"
MutUtils.removeDir(download_dir)
os.mkdir(download_dir)
GenomeBuildInstallUtils.download_reference_data_from_ensembl(download_dir, "saccharomyces_cerevisiae")
downloaded_files = os.listdir(download_dir)
transcript_file = None
for f in downloaded_files:
if f.find(".cdna.") != -1:
transcript_file = f
break
self.assertIsNotNone(transcript_file)
statinfo = os.stat(download_dir + transcript_file)
self.assertTrue(statinfo.st_size > 0, "downloaded transcript file (" + transcript_file + ") is empty.")
def test_previous_release_download(self):
"""Download an older ensembl transcript package. This test needs an internet connection and will fail w/o one.
"""
download_dir = "out/test_ensembl_download_previous/"
release_num = "68"
MutUtils.removeDir(download_dir)
os.mkdir(download_dir)
GenomeBuildInstallUtils.download_reference_data_from_ensembl(
download_dir, "saccharomyces_cerevisiae", release=release_num)
downloaded_files = os.listdir(download_dir)
transcript_file = None
for f in downloaded_files:
if f.find("." + release_num + ".cdna.") != -1:
transcript_file = f
break
self.assertIsNotNone(transcript_file)
statinfo = os.stat(download_dir + transcript_file)
self.assertTrue(
statinfo.st_size > 0,
"downloaded transcript file (" + transcript_file + ") is empty.")
def test_current_download(self):
"""Download a current ensembl transcript package. This test needs an internet connection and can be slow."""
#ftp://ftp.ensembl.org/pub/release-71/fasta/saccharomyces_cerevisiae/cdna/
download_dir = "out/test_ensembl_download/"
MutUtils.removeDir(download_dir)
os.mkdir(download_dir)
GenomeBuildInstallUtils.download_reference_data_from_ensembl(
download_dir, "saccharomyces_cerevisiae")
downloaded_files = os.listdir(download_dir)
transcript_file = None
for f in downloaded_files:
if f.find(".cdna.") != -1:
transcript_file = f
break
self.assertIsNotNone(transcript_file)
statinfo = os.stat(download_dir + transcript_file)
self.assertTrue(
statinfo.st_size > 0,
"downloaded transcript file (" + transcript_file + ") is empty.")
# Setup argument parser
epilog = '''
Supported species:
''' + "\n\t".join(VALID_ENSEMBL_SPECIES)
desc = ''' Download ENSEMBL files from FTP server. Please see -h for supported species list.
'''
parser = ArgumentParser(description=desc,
formatter_class=RawDescriptionHelpFormatter,
epilog=epilog)
parser.add_argument('speciesName', type=str, help="Species name")
parser.add_argument('downloadDir',
type=str,
help="Where to download files.")
# Process arguments
args = parser.parse_args()
return args
if __name__ == "__main__":
args = parseOptions()
species = args.speciesName
destDir = args.downloadDir
if not os.path.exists(destDir):
os.makedirs(destDir)
GenomeBuildInstallUtils.download_reference_data_from_ensembl(
destDir, species)
__author__ = 'lichtens'
from oncotator.utils.install.GenomeBuildInstallUtils import GenomeBuildInstallUtils
from oncotator.utils.install.GenomeBuildInstallUtils import VALID_ENSEMBL_SPECIES
def parseOptions():
# Setup argument parser
epilog= '''
Supported species:
''' + "\n\t".join(VALID_ENSEMBL_SPECIES)
desc = ''' Download ENSEMBL files from FTP server. Please see -h for supported species list.
'''
parser = ArgumentParser(description=desc, formatter_class=RawDescriptionHelpFormatter, epilog=epilog)
parser.add_argument('speciesName', type=str, help="Species name")
parser.add_argument('downloadDir', type=str, help="Where to download files.")
# Process arguments
args = parser.parse_args()
return args
if __name__ == "__main__":
args = parseOptions()
species = args.speciesName
destDir = args.downloadDir
if not os.path.exists(destDir):
os.makedirs(destDir)
GenomeBuildInstallUtils.download_reference_data_from_ensembl(destDir, species)
