def main():
requiredExecutables = ['gunzip', 'bgzip', 'samtools']
utils.requireExecutables(requiredExecutables)
args = parseArgs()
fastaFileName = decompressFasta(args)
splitFileNames = splitFasta(fastaFileName)
compressedFileNames = compressSplits(splitFileNames)
indexSplits(compressedFileNames)
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(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()
