def download_chromosomes(self):
to_download = self.get_missing_chromosomes()
self.log("Downloading {} chromosomes".format(len(to_download)))
for name in to_download:
chromosome = Chromosome(name, self.assembly)
self.log(chromosome.path())
path = chromosome.path()
directory = os.path.dirname(chromosome.path())
if not os.path.isdir(directory):
os.makedirs(directory)
self.log('Created directory {}'.format(directory), True)
self.log('Downloading {}{} to {}'.format(self.uri,
chromosome.filename(),
path),
force=True)
r = requests.get(self.uri + chromosome.filename(), stream=True)
with open(path, 'wb') as fd:
for chunk in r.iter_content(chunk_size=1024):
fd.write(chunk)
self.log('Complete', True)
run_build_test_suite(self.assembly)
def download_chromosome(self, name):
chromosome = Chromosome(name, self.assembly)
path = chromosome.path()
directory = os.path.dirname(chromosome.path())
if not os.path.isdir(directory):
os.makedirs(directory)
self.log('Created directory {}'.format(directory), True)
uri = URI + chromosome.filename()
self.log(
'Downloading from {} to {}'.format(uri, path), True)
r = requests.get(uri, stream=True)
# TODO can we do this in fewer than 3 passes?
with open(path, 'wb') as fd:
for chunk in r.iter_content(chunk_size=1024):
fd.write(chunk)
with open(path, 'r') as f:
header = f.readline()
content = f.read().replace('\n', '')
with open(path, 'w') as f:
f.write(header)
f.write(content)
f.write('\n')
self.log('...Complete', True)
def download_chromosome(self, name):
chromosome = Chromosome(name, self.assembly)
path = chromosome.path()
directory = os.path.dirname(chromosome.path())
if not os.path.isdir(directory):
os.makedirs(directory)
self.log('Created directory {}'.format(directory), True)
uri = URI + chromosome.filename()
self.log('Downloading from {} to {}'.format(uri, path), True)
r = requests.get(uri, stream=True)
# TODO can we do this in fewer than 3 passes?
with open(path, 'wb') as fd:
for chunk in r.iter_content(chunk_size=1024):
fd.write(chunk)
with open(path, 'r') as f:
header = f.readline()
content = f.read().replace('\n', '')
with open(path, 'w') as f:
f.write(header)
f.write(content)
f.write('\n')
self.log('...Complete', True)
def download_chromosomes(self):
to_download = self.get_missing_chromosomes()
self.log("Downloading {} chromosomes".format(len(to_download)))
for name in to_download:
chromosome = Chromosome(name, self.assembly)
self.log(chromosome.path())
path = chromosome.path()
directory = os.path.dirname(chromosome.path())
if not os.path.isdir(directory):
os.makedirs(directory)
self.log('created directory {}'.format(directory), True)
self.log('Downloading {} to {}'.format(self.uri + chromosome.filename(), path))
r = requests.get(self.uri + chromosome.filename(), stream=True)
with open(path, 'wb') as fd:
for chunk in r.iter_content(chunk_size=1024):
fd.write(chunk)
self.log('Complete')
run_build_test_suite(self.assembly)
