def main(): requiredExecutables = ['gunzip', 'bgzip', 'samtools'] utils.requireExecutables(requiredExecutables) args = parseArgs() fastaFileName = decompressFasta(args) splitFileNames = splitFasta(fastaFileName) compressedFileNames = compressSplits(splitFileNames) indexSplits(compressedFileNames)
def main(args): requiredExecutables = ['bcftools', 'tabix', 'bgzip', 'samtools'] utils.requireExecutables(requiredExecutables) downloaderClass = sources[args.source] downloader = downloaderClass(args) try: downloader.downloadVcfs() downloader.downloadReference() downloader.downloadBams() downloader.createRepo() finally: downloader.cleanup()
def main(): requiredExecutables = ['bgzip', 'samtools'] utils.requireExecutables(requiredExecutables) parser = argparse.ArgumentParser( description="Generate random FASTA files and metadata") parser.add_argument("output_prefix", help="The prefix for generated files.") basesDefault = 1000 parser.add_argument( "--num-bases", "-n", default=basesDefault, help="number of bases to include; default {}".format(basesDefault)) fastaGenerator = FastaGenerator(parser.parse_args()) fastaGenerator.generate()