def main(config_file):
with open(config_file) as in_handle:
config = yaml.load(in_handle)
create_dirs(config)
with cpmap(config["algorithm"]["cores"]) as cur_map:
for _ in cur_map(process_fastq, ((fastq, ref_index, config, config_file)
for fastq, ref_index in fastq_to_process(config))):
pass
def main(config_file):
with open(config_file) as in_handle:
config = yaml.load(in_handle)
create_dirs(config)
with cpmap(config["algorithm"]["cores"]) as cur_map:
for _ in cur_map(process_fastq, ((fastq, ref_index, config, config_file)
for fastq, ref_index in fastq_to_process(config))):
pass
def main(config_file):
with open(config_file) as in_handle:
config = yaml.load(in_handle)
utils.create_dirs(config)
clean_cdna = clean_vector(config["cdna_reads"], config)
cluster_cdna = cluster_seqs(clean_cdna, config)
tl_stats = translation_stats(cluster_cdna, config)
for ref in config["ref"]:
cmp_file = process_ref(cluster_cdna, ref, config)
display_tl_results(ref, cmp_file, tl_stats, config)
write_tl_nohit(cluster_cdna, cmp_file, tl_stats, ref, config)
annotated_refs(cmp_file, ref, config)
def main(config_file):
with open(config_file) as in_handle:
config = yaml.load(in_handle)
utils.create_dirs(config)
clean_cdna = clean_vector(config["cdna_reads"], config)
cluster_cdna = cluster_seqs(clean_cdna, config)
tl_stats = translation_stats(cluster_cdna, config)
for ref in config["ref"]:
cmp_file = process_ref(cluster_cdna, ref, config)
display_tl_results(ref, cmp_file, tl_stats, config)
write_tl_nohit(cluster_cdna, cmp_file, tl_stats, ref, config)
annotated_refs(cmp_file, ref, config)
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
