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)