def main(config_file):
with open(config_file) as in_handle:
config = yaml.load(in_handle)
ref_index = novoalign.refindex(config["ref"], kmer_size=13, step_size=1)
create_dirs(config)
for cur in config["input"]:
in_fastq = cur["fastq"]
if cur.get("old_style_barcodes", False):
in_fastq = convert_illumina_oldstyle(in_fastq)
bc_files = demultiplex(in_fastq, cur["barcodes"],
config["dir"]["tmp"], config)
with cpmap(config["algorithm"]["cores"]) as cur_map:
for _ in cur_map(process_fastq, ((bc_file, ref_index, cur, config, config_file)
for bc_file in bc_files)):
pass
def _index_ref_genome(config, cur):
ref = config.get("ref", cur.get("ref", None))
return novoalign.refindex(ref, kmer_size=13, step_size=1)
def _index_ref_genome(config, cur):
ref = config.get("ref", cur.get("ref", None))
return novoalign.refindex(ref, kmer_size=13, step_size=1)