def execute(run, output_filename):
for dirname in os.listdir(run["path"]):
# To check it is dir, not file
if os.path.isdir(run["path"] + dirname):
# BaseSpace (Illumina) directory structure
data_path = (run["path"] + dirname +
"/Data/Intensities/BaseCalls/")
sample = dir_tools.get_sample_info(run["path"] + dirname)
prefix = run["name"] + "_" + sample["num"]
varscan_results = run_varscan(
prefix,
data_path)
if varscan_results != "no reads.":
annotate_results(varscan_results,
output_filename,
sample["num"],
sample["name"],
data_path + prefix)
def main(shell_args):
global MODE, OUTPUT_FILENAME
MODE = str.upper(shell_args.mode)
OUTPUT_FILENAME = shell_args.output_filename
run = dir_tools.get_run_info(shell_args.run_path)
init_output()
for dirname in os.listdir(run['path']):
# To check it is dir, not file
if os.path.isdir(run['path'] + dirname):
# BaseSpace (Illumina) directory structure
data_path = (run['path'] + dirname +
'/Data/Intensities/BaseCalls/')
sample = dir_tools.get_sample_info(run['path'] + dirname)
prefix = run['name'] + '_' + sample['num']
if MODE == 'READS':
run_reads(data_path, sample, prefix)
elif MODE == 'VARIANTS':
run_variants(data_path, sample, prefix)