def main(system_config_file, cur_config_file):
config = utils.merge_config_files([system_config_file, cur_config_file])
run_module = "bcbio.hbc.linker"
trim_vals = config["algorithm"]["simple_trims"]
fastq_dir = utils.add_full_path(config["dir"]["fastq"])
cur_files = [
os.path.join(fastq_dir, x["file"]) for x in config["experiments"]
]
dirs = {
"config": utils.add_full_path(os.path.dirname(system_config_file)),
"work": os.getcwd(),
"align": utils.add_full_path(config["dir"]["align"])
}
dirs["galaxy"] = os.path.dirname(
utils.add_full_path(config["galaxy_config"], dirs["config"]))
config["dir"]["trim"] = utils.add_full_path(config["dir"]["work_trim"])
config["dir"]["fastq"] = fastq_dir
config["dir"]["work_fastq"] = utils.add_full_path(
config["dir"]["work_fastq"])
run_parallel = parallel_runner(run_module, dirs, config,
system_config_file)
aligned = []
for i in range(len(trim_vals.values()[0])):
print cur_files
in_args = [(f, i, trim_vals, config) for f in cur_files]
align_trimmed_files = run_parallel("trim_with_aligner", in_args)
cur_files = [
x["unaligned"] for x in align_trimmed_files if x["unaligned"]
]
aligned.append([x["aligned"] for x in align_trimmed_files])
trimmed_fastq = combine_aligned(aligned, config)
align_bams = do_alignment(trimmed_fastq, config, dirs, run_parallel)
count_files = count_targets(align_bams, config)
combine.identify_top_ranked(count_files, config)
def main(system_config_file, cur_config_file):
config = utils.merge_config_files([system_config_file, cur_config_file])
run_module = "bcbio.hbc.linker"
trim_vals = config["algorithm"]["simple_trims"]
fastq_dir = utils.add_full_path(config["dir"]["fastq"])
cur_files = [os.path.join(fastq_dir, x["file"]) for x in config["experiments"]]
dirs = {"config": utils.add_full_path(os.path.dirname(system_config_file)),
"work" : os.getcwd(),
"align": utils.add_full_path(config["dir"]["align"])}
dirs["galaxy"] = os.path.dirname(utils.add_full_path(config["galaxy_config"], dirs["config"]))
config["dir"]["trim"] = utils.add_full_path(config["dir"]["work_trim"])
config["dir"]["fastq"] = fastq_dir
config["dir"]["work_fastq"] = utils.add_full_path(config["dir"]["work_fastq"])
run_parallel = parallel_runner(run_module, dirs, config, system_config_file)
aligned = []
for i in range(len(trim_vals.values()[0])):
print cur_files
in_args = [(f, i, trim_vals, config) for f in cur_files]
align_trimmed_files = run_parallel("trim_with_aligner", in_args)
cur_files = [x["unaligned"] for x in align_trimmed_files if x["unaligned"]]
aligned.append([x["aligned"] for x in align_trimmed_files])
trimmed_fastq = combine_aligned(aligned, config)
align_bams = do_alignment(trimmed_fastq, config, dirs, run_parallel)
count_files = count_targets(align_bams, config)
combine.identify_top_ranked(count_files, config)
def main(system_config_file, cur_config_file):
config = utils.merge_config_files([system_config_file, cur_config_file])
workers_needed = len(config["experiments"])
task_module = "bcbio.hbc.linker.tasks"
queue = "hbc.trim"
args = [system_config_file, cur_config_file]
run_and_monitor(config, system_config_file, args, workers_needed, task_module,
queues=queue)
def main(system_config_file, cur_config_file):
config = utils.merge_config_files([system_config_file, cur_config_file])
workers_needed = len(config["experiments"])
task_module = "bcbio.hbc.linker.tasks"
queue = "hbc.trim"
args = [system_config_file, cur_config_file]
run_and_monitor(config,
system_config_file,
args,
workers_needed,
task_module,
queues=queue)
