def run_gc_depth(genome, fastq_list, name, window, thread, job_type,
concurrent, refresh, work_dir, out_dir):
genome, fastq_list = check_paths([genome, fastq_list])
sort_bam, genome = bwa_mem(fastq_list=fastq_list,
genome=genome,
name=name,
number=5000000,
data_type='',
thread=thread,
job_type=job_type,
concurrent=concurrent,
refresh=refresh,
work_dir=work_dir,
out_dir=work_dir)
sort_bam = check_paths(sort_bam)
dag = DAG("gc_depth")
gc_depth_task, gc_depth_png = stat_gc_depth_task(genome=genome,
bam=sort_bam,
name=name,
window=window,
job_type=job_type,
work_dir=work_dir,
out_dir=out_dir)
dag.add_task(gc_depth_task)
do_dag(dag, concurrent, refresh)
return gc_depth_png
def run_ncovann(genomes, refgff, concurrent, refresh, job_type, work_dir,
out_dir):
genomes = check_paths(genomes)
refgff = check_path(refgff)
work_dir = mkdir(work_dir)
out_dir = mkdir(out_dir)
dag = DAG("ncovann")
for genome in genomes:
name = genome.split('/')[-1]
if '--' in name:
name = name.split('--')[0].split('.')[0]
else:
name = name.split('.')[0]
ann_task = create_ncovann_task(genome=genome,
name=name,
refgff=refgff,
job_type=job_type,
work_dir=work_dir,
out_dir=out_dir)
dag.add_task(ann_task)
do_dag(dag, concurrent, refresh)
return 0
def choose_data(r1, r2, name, kmer_length, kmer_depth, thread, job_type, concurrent, refresh, work_dir, out_dir):
r1, r2, kmer_stat, option = stat_kmer_depth(
r1=r1,
r2=r2,
name=name,
kmer_length=kmer_length,
thread=thread,
job_type=job_type,
concurrent=concurrent,
refresh=refresh,
work_dir=work_dir,
out_dir=out_dir)
dag = DAG("choose_data")
data_task, r1, r2 = choose_data_task(
r1=r1,
r2=r2,
name=name,
kmer_stat=kmer_stat,
kmer_depth=kmer_depth,
job_type=job_type,
work_dir=work_dir,
out_dir=out_dir)
dag.add_task(data_task)
do_dag(dag, concurrent, refresh)
return option, r1, r2
def run_ncovsnp(reads,
reffa,
refgb,
thread,
concurrent,
refresh,
job_type,
work_dir,
out_dir,
clean=""):
reads = check_paths(reads)
reffa = check_path(reffa)
refgb = check_path(refgb)
work_dir = mkdir(work_dir)
out_dir = mkdir(out_dir)
options = {"software": OrderedDict(), "database": OrderedDict()}
dag = DAG("ncovsnp")
option = OrderedDict()
depths = os.path.join(work_dir, "*/*.depth.xls")
snps = os.path.join(work_dir, "*/*.snps.gff")
stat_map_task = stat_mapcover_snp(reads=' '.join(reads),
clean=clean,
depths=depths,
snps=snps,
job_type="local",
work_dir=work_dir,
out_dir=out_dir)
genomes = []
for read in reads:
name = read.split('/')[-1]
if '--' in name:
name = name.split('--')[0].split('.')[0]
else:
name = name.split('.')[0]
name_work = mkdir(os.path.join(work_dir, name))
snp_task, snippy_task, concencus, option = create_ncovsnp_tasks(
read=read,
name=name,
reffa=reffa,
refgb=refgb,
thread=thread,
job_type=job_type,
work_dir=name_work,
out_dir=out_dir)
genomes.append(concencus)
dag.add_task(snp_task)
dag.add_task(snippy_task)
stat_map_task.set_upstream(snp_task)
stat_map_task.set_upstream(snippy_task)
options["software"] = option
dag.add_task(stat_map_task)
do_dag(dag, concurrent, refresh)
return genomes, options
def split_data(r1, r2, name, number, job_type, concurrent, refresh, work_dir, out_dir, platform="illumina"):
if platform in ["PromethION", "GridION" , "RSII", "Sequel"]:
read = "%s.part_*.fast*" % name
r2 = ""
elif platform in ["illumina", "mgi"]:
read = "%s.r1.part_*.fastq" % name
else:
raise Exception("The input sequencing platform is abnormal.")
dag = DAG("split_data")
task = Task(
id="split_data",
work_dir=work_dir,
type=job_type,
option="-pe smp 1",
script="""
{script}/splitfp.py -r1 {r1} -r2 {r2} -o {name} -n {number}
#cp {name}.* {out_dir}
""".format(
script=SCRIPTS,
r1=r1,
r2=r2,
name=name,
number=number,
out_dir=out_dir
)
)
dag.add_task(task)
do_dag(dag, concurrent, refresh)
temp = read_files(work_dir, read)
reads = []
if platform in ["illumina", "mgi"]:
for i in temp:
j = i.replace(".r1.part_", ".r2.part_")
reads.append("%s %s" % (i, j))
else:
reads = temp
return reads
def bwa_mem(fastq_list, genome, name, number, data_type, thread, job_type,
concurrent, refresh, work_dir, out_dir):
genome, fastq_list = check_paths([genome, fastq_list])
work_dir = mkdir(work_dir)
out_dir = mkdir(out_dir)
dag = DAG("split_ngs")
split_work = mkdir(os.path.join(work_dir, "00_data"))
split_out = mkdir(os.path.join(out_dir, "00_data"))
splitfp_task, fq_path, r1_name, r2_name = split_ngs_task(
fastq_list=fastq_list,
name=name,
number=number,
data_type=data_type,
job_type=job_type,
work_dir=split_work,
out_dir=split_out)
dag.add_task(splitfp_task)
do_dag(dag, concurrent, refresh)
dag = DAG("bwa_mem")
index_task, bwa_tasks, merge_task, sorted_bam, genome = run_bwa_mem(
fq_path=fq_path,
r1_name=r1_name,
r2_name=r2_name,
genome=genome,
name=name,
thread=thread,
job_type=job_type,
work_dir=work_dir,
out_dir=out_dir)
dag.add_task(index_task)
dag.add_task(*bwa_tasks)
dag.add_task(merge_task)
index_task.set_downstream(*bwa_tasks)
merge_task.set_upstream(*bwa_tasks)
do_dag(dag, concurrent, refresh)
return sorted_bam, genome
def stat_kmer_depth(r1, r2, name, kmer_length, thread, job_type, concurrent, refresh, work_dir, out_dir):
dag = DAG("survey_data")
data_task, r1, r2 = merge_data_task(
name=name,
r1=r1,
r2=r2,
job_type=job_type,
work_dir=work_dir,
out_dir=out_dir)
kmerfreq_task, kmer_stat, option= create_kmerfreq_task(
r1=r1,
r2=r2,
name=name,
kmer_length=kmer_length,
thread=thread,
job_type=job_type,
work_dir=work_dir,
out_dir=out_dir)
dag.add_task(data_task)
dag.add_task(kmerfreq_task)
kmerfreq_task.set_upstream(data_task)
do_dag(dag, concurrent, refresh)
return r1, r2, kmer_stat, option
def split_data(r1, r2, name, number, job_type, work_dir, out_dir):
if len(r1) != len(r2) and len(r2) <= 1:
read = "%s.part_*.fast*" % name
r2 = ""
elif len(r1) == len(r2):
read = "%s.r1.part_*.fastq" % name
else:
raise Exception("The input sequencing platform is abnormal.")
dag = DAG("split_data")
task = Task(id="split_data",
work_dir=work_dir,
type=job_type,
option="-pe smp 1",
script="""
{script}/splitfp.py -r1 {r1} -r2 {r2} -o {name} -n {number}
#cp {name}.* {out_dir}
""".format(script=SCRIPTS,
r1=r1,
r2=r2,
name=name,
number=number,
out_dir=out_dir))
dag.add_task(task)
do_dag(dag, 8, 10)
temp = read_files(work_dir, read)
reads = []
if len(r1) == len(r2):
for i in temp:
j = i.replace(".r1.part_", ".r2.part_")
reads.append("%s %s" % (i, j))
else:
reads = temp
return reads
def run_gc_depth(genome, r1, r2, name, platform, split, window, thread,
job_type, concurrent, refresh, work_dir, out_dir):
genome = check_path(genome)
r1 = check_paths(r1)
r2 = check_paths(r2)
sort_bam = minimap(r1=r1,
r2=r2,
genome=genome,
name=name,
split=split,
platform=platform,
number=5000000,
thread=thread,
job_type=job_type,
concurrent=concurrent,
refresh=refresh,
work_dir=work_dir,
out_dir=out_dir)
sort_bam = check_paths(sort_bam)
dag = DAG("gc_depth")
gc_depth_task, gc_depth_png = stat_gc_depth_task(genome=genome,
bam=sort_bam,
name=name,
window=window,
job_type=job_type,
work_dir=work_dir,
out_dir=out_dir)
dag.add_task(gc_depth_task)
do_dag(dag, concurrent, refresh)
return gc_depth_png
def run_ncovqc(reads, reference, thread, job_type, concurrent, refresh,
work_dir, out_dir):
reference = check_path(reference)
work_dir = mkdir(work_dir)
out_dir = mkdir(out_dir)
reads = check_paths(reads)
names = []
for i in reads:
name = i.split('/')[-1]
if '--' in name:
name = name.split('--')[1].split('.bam')[0]
else:
name = name.split('.')[0]
names.append(name)
options = {"software": OrderedDict(), "database": OrderedDict()}
dag = DAG("ncovqc")
raw_task, raw_stat = stat_reads_task(reads=" ".join(reads),
name="raw",
thread=thread,
job_type=job_type,
work_dir=work_dir,
out_dir=out_dir)
map_tasks, clean_reads, option = map_ref_tasks(reads=reads,
names=names,
reference=reference,
thread=thread,
job_type=job_type,
work_dir=work_dir,
out_dir=out_dir)
options["software"] = option
clean_task, clean_stat = stat_reads_task(reads=clean_reads,
name="clean",
thread=thread,
job_type=job_type,
work_dir=work_dir,
out_dir=out_dir)
dag.add_task(raw_task)
dag.add_task(*map_tasks)
dag.add_task(clean_task)
clean_task.set_upstream(*map_tasks)
do_dag(dag, concurrent, refresh)
return clean_reads, clean_stat, options
def run_minimap(reads, genome, platform, name, split, thread, job_type,
concurrent, refresh, work_dir, out_dir):
option = OrderedDict()
option["minimap2"] = {
"version": get_version(SOFTWARE_VERSION["minimap2"]),
"option": "%s" % SEQUENCER[platform]["minimap2"]
}
work_dict = {"minimap": "01_minimap", "merge": "02_merge"}
for k, v in work_dict.items():
mkdir(os.path.join(work_dir, v))
dag = DAG("minimap")
minimap_tasks, bams = create_minimap_tasks(reads=reads,
genome=genome,
platform=platform,
name=name,
thread=thread,
job_type=job_type,
work_dir=os.path.join(
work_dir,
work_dict["minimap"]),
out_dir=out_dir,
split=split)
merge_task, bam = merge_bam_task(bams=bams,
name=name,
thread=thread,
job_type=job_type,
work_dir=os.path.join(
work_dir, work_dict["merge"]),
out_dir=out_dir)
dag.add_task(*minimap_tasks)
dag.add_task(merge_task)
merge_task.set_upstream(*minimap_tasks)
do_dag(dag, concurrent, refresh)
return bam, option
def run_survey(r1, r2, name, trim, kingdom, kmer_length, sample_depth, thread,
asm, window, job_type, queue, concurrent, refresh, work_dir,
out_dir):
work_dir = mkdir(work_dir)
out_dir = mkdir(out_dir)
r1 = check_paths(r1)
r2 = check_paths(r2)
dag = DAG("survey_qc")
merge_task, qc_task, cont_task, result_task, clean1, clean2, quality, content, gc, stat_qc, poll_png, poll_tsv = ngs_qc_tasks(
name=name,
r1=r1,
r2=r2,
trim=trim,
thread=thread,
job_type=job_type,
work_dir=work_dir,
out_dir=out_dir)
data_work = mkdir(os.path.join(work_dir, "choose_data"))
freq_task1, histo1, kmer_stat, estimate1 = kmerfreq_task(
r1=clean1,
r2=clean2,
name=name,
kmer_length=kmer_length,
thread=thread,
job_type=job_type,
work_dir=data_work,
out_dir=data_work)
dag.add_task(merge_task)
dag.add_task(qc_task)
qc_task.set_upstream(merge_task)
dag.add_task(cont_task)
dag.add_task(result_task)
dag.add_task(freq_task1)
freq_task1.set_upstream(qc_task)
cont_task.set_upstream(qc_task)
result_task.set_upstream(qc_task)
do_dag(dag, concurrent, refresh)
for line in read_tsv(kmer_stat):
if line[0] == "kmer_depth":
kmer_depth = int(line[1])
if sample_depth > kmer_depth:
LOG.debug(
'The amount of sequencing data may be insufficient. Sequencing depth is only %s X'
% kmer_depth)
sample_depth = kmer_depth
proportion = sample_depth * 1.0 / kmer_depth
dag = DAG("survey")
choose_task, freq_task, heter_task, jellyfish_task, gse_scope_task, denovo_task, stat_heter, heter_png, scope_txt, gse_txt, scope_png, gse_png, stat_genome, genome, ngs_list = kmer_denovo_tasks(
r1=clean1,
r2=clean2,
name=name,
kmer_length=kmer_length,
proportion=proportion,
kingdom=kingdom,
thread=thread,
job_type=job_type,
queue=queue,
work_dir=work_dir,
out_dir=out_dir)
if asm == "true":
dag.add_task(denovo_task)
else:
genome = "false"
stat_genome = "false"
ngs_list = "false"
dag.add_task(choose_task)
dag.add_task(freq_task)
dag.add_task(heter_task)
freq_task.set_upstream(choose_task)
dag.add_task(jellyfish_task)
jellyfish_task.set_upstream(choose_task)
dag.add_task(gse_scope_task)
heter_task.set_upstream(freq_task)
gse_scope_task.set_upstream(jellyfish_task)
do_dag(dag, concurrent, refresh)
if ngs_list == "false":
print("Genomics are not assembled")
gc_depth_png = heter_png
else:
depth_work = mkdir(os.path.join(work_dir, "05_GC-depth"))
depth_out = mkdir(os.path.join(out_dir, "05_GC-depth"))
gc_depth_png = run_gc_depth(genome=genome,
fastq_list=ngs_list,
name=name,
window=window,
thread=thread,
job_type=job_type,
concurrent=concurrent,
refresh=refresh,
work_dir=depth_work,
out_dir=depth_out)
run_report(name, asm, kmer_length, stat_qc, quality, content, gc, poll_tsv,
poll_png, stat_heter, heter_png, scope_txt, gse_txt, scope_png,
gse_png, stat_genome, gc_depth_png, out_dir)
return stat_qc, quality, content, gc, poll_png, poll_tsv, stat_heter, heter_png, scope_txt, gse_txt, scope_png, gse_png, stat_genome
def run_filter_contamination(r1, r2, name, kmer_length, kmer_depth, taxid, kingdom, thread, job_type, concurrent, refresh, work_dir, out_dir, split, mode="fast", cratio=10):
work_dir = mkdir(work_dir)
out_dir = mkdir(out_dir)
r1 = check_paths(r1)
r2 = check_paths(r2)
taxid = check_path(taxid)
options = {
"software": OrderedDict(),
"database": OrderedDict()
}
option, r1, r2 = choose_data(
r1=r1,
r2=r2,
name=name,
kmer_length=kmer_length,
kmer_depth=kmer_depth,
thread=thread,
job_type=job_type,
concurrent=concurrent,
refresh=refresh,
work_dir=work_dir,
out_dir=out_dir)
options["software"].update(option)
if mode!="fast":
work_dict = {
"data": "00_data",
"ref": "01_ref",
"ump": "02_ump"
}
for k, v in work_dict.items():
mkdir(os.path.join(work_dir, v))
reads = split_data(
r1=r1,
r2=r2,
name=name,
number=2000000,
job_type=job_type,
work_dir=os.path.join(work_dir, work_dict["data"]),
concurrent=concurrent,
refresh=refresh,
out_dir=out_dir,
platform="illumina")
dag = DAG("unmap_data")
ref_task, ref= obtain_contamination_task(
taxid=taxid,
name=name,
kingdom=kingdom,
job_type=job_type,
work_dir=os.path.join(work_dir, work_dict["ref"]),
out_dir=out_dir,
mode=mode,
cratio=cratio)
dag.add_task(ref_task)
unmap_tasks, reads, option = create_unmap_tasks(
name=name,
reference=ref,
reads=reads,
thread=thread,
job_type=job_type,
work_dir=os.path.join(work_dir, work_dict["ump"]),
out_dir=out_dir,
split=split)
dag.add_task(*unmap_tasks)
ref_task.set_downstream(*unmap_tasks)
do_dag(dag, concurrent, refresh)
options["software"].update(option)
reads = [reads]
else:
reads = [r1, r2]
return reads, options
def run_kmer_denovo(r1, r2, name, kingdom, kmer_length, sample_depth, thread,
asm, window, job_type, queue, concurrent, refresh,
work_dir, out_dir):
work_dir = mkdir(work_dir)
out_dir = mkdir(out_dir)
r1 = check_paths(r1)
r2 = check_paths(r2)
if r1[0].endswith(".gz") or r2[0].endswith(".gz"):
tools = "zcat"
else:
tools = "cat"
dag_data = DAG("survey_data")
data_work = mkdir(os.path.join(work_dir, "choose_data"))
cat_data_task, clean1, clean2 = merge_raw_data_task(name=name,
r1=" ".join(r1),
r2=" ".join(r2),
tools=tools,
job_type=job_type,
work_dir=data_work,
out_dir=data_work)
freq_task1, histo1, kmer_stat, estimate1 = kmerfreq_task(
r1=clean1,
r2=clean2,
name=name,
kmer_length=17,
thread=thread,
job_type=job_type,
work_dir=data_work,
out_dir=data_work)
dag_data.add_task(cat_data_task)
dag_data.add_task(freq_task1)
freq_task1.set_upstream(cat_data_task)
do_dag(dag_data, concurrent, refresh)
for line in read_tsv(kmer_stat):
if line[0] == "kmer_depth":
kmer_depth = int(line[1])
if sample_depth > kmer_depth:
LOG.debug(
'The amount of sequencing data may be insufficient. Sequencing depth is only %s X'
% kmer_depth)
sample_depth = kmer_depth
proportion = sample_depth * 1.0 / kmer_depth
dag = DAG("survey")
choose_task, freq_task, heter_task, jellyfish_task, gse_scope_task, denovo_task, stat_heter, heter_png, scope_txt, gse_txt, scope_png, gse_png, stat_genome, genome, ngs_list = kmer_denovo_tasks(
r1=clean1,
r2=clean2,
name=name,
kmer_length=kmer_length,
proportion=proportion,
kingdom=kingdom,
thread=thread,
job_type=job_type,
queue=queue,
work_dir=work_dir,
out_dir=out_dir)
if asm == "true":
dag.add_task(denovo_task)
else:
genome = "false"
stat_genome = "false"
ngs_list = "false"
dag.add_task(choose_task)
dag.add_task(freq_task)
dag.add_task(heter_task)
freq_task.set_upstream(choose_task)
dag.add_task(jellyfish_task)
jellyfish_task.set_upstream(choose_task)
dag.add_task(gse_scope_task)
heter_task.set_upstream(freq_task)
gse_scope_task.set_upstream(jellyfish_task)
do_dag(dag, concurrent, refresh)
if ngs_list == "false":
print("Genomics are not assembled")
gc_depth_png = heter_png
else:
depth_work = mkdir(os.path.join(work_dir, "05_GC-depth"))
depth_out = mkdir(os.path.join(out_dir, "05_GC-depth"))
gc_depth_png = run_gc_depth(genome=genome,
fastq_list=ngs_list,
name=name,
window=window,
thread=thread,
job_type=job_type,
concurrent=concurrent,
refresh=refresh,
work_dir=depth_work,
out_dir=depth_out)
return stat_heter, heter_png, scope_txt, gse_txt, scope_png, gse_png, stat_genome
def run_kmer_denovo(r1,
r2,
taxid,
name,
mode,
cratio,
kmer_length,
kmer_depth,
kingdom,
asm,
window,
thread,
job_type,
queue,
concurrent,
refresh,
work_dir,
out_dir,
split,
platform="illumina"):
work_dir = mkdir(work_dir)
out_dir = mkdir(out_dir)
r1 = check_paths(r1)
r2 = check_paths(r2)
work_dict = {
"contamination": "01_contamination",
"gse_scope": "02_gse_scope",
"kmerfreq": "03_Kmerfreq",
"denovo": "04_Soapdenovo",
"gc_depth": "05_GC-depth"
}
for k, v in work_dict.items():
mkdir(os.path.join(work_dir, v))
if k == "contamination":
continue
mkdir(os.path.join(out_dir, v))
reads, options = run_filter_contamination(r1=r1,
r2=r2,
name=name,
kmer_length=kmer_length,
kmer_depth=kmer_depth,
taxid=taxid,
kingdom=kingdom,
thread=thread,
job_type=job_type,
concurrent=concurrent,
refresh=refresh,
work_dir=os.path.join(
work_dir,
work_dict["contamination"]),
out_dir=out_dir,
mode=mode,
cratio=cratio,
split=split)
dag = DAG("kmer_denovo")
jellyfish_task, gse_scope_task, scope_txt, gse_txt, scope_png, gse_png, option = gse_scope(
reads=" ".join(reads),
name=name,
kmer_length=kmer_length,
thread=thread,
job_type=job_type,
work_dir=os.path.join(work_dir, work_dict["gse_scope"]),
out_dir=os.path.join(out_dir, work_dict["gse_scope"]),
mode=mode)
options["software"].update(option)
dag.add_task(jellyfish_task)
dag.add_task(gse_scope_task)
kmerfreq_task, heter_task, stat_heter, heter_png, option = kmerfreq(
reads=" ".join(reads),
name=name,
kingdom=kingdom,
kmer_length=kmer_length,
thread=thread,
job_type=job_type,
work_dir=os.path.join(work_dir, work_dict["kmerfreq"]),
out_dir=os.path.join(out_dir, work_dict["kmerfreq"]))
options["software"].update(option)
dag.add_task(kmerfreq_task)
dag.add_task(heter_task)
denovo_task, genome, stat_genome, option = create_soapdenovo_task(
r1=" ".join(r1),
r2=" ".join(r2),
name=name,
thread=thread,
queue=queue,
job_type=job_type,
work_dir=os.path.join(work_dir, work_dict["denovo"]),
out_dir=os.path.join(out_dir, work_dict["denovo"]))
if asm == "true":
dag.add_task(denovo_task)
else:
genome = "false"
stat_genome = "false"
do_dag(dag, concurrent, refresh)
if asm == "true":
gc_depth = run_gc_depth(genome=genome,
r1=" ".join(r1),
r2=" ".join(r2),
name=name,
platform=platform,
split="no_split",
window=window,
thread=thread,
job_type=job_type,
concurrent=concurrent,
refresh=refresh,
work_dir=os.path.join(work_dir,
work_dict["gc_depth"]),
out_dir=os.path.join(out_dir,
work_dict["gc_depth"]))
else:
gc_depth = heter_png
with open(os.path.join(out_dir, "kmer_denovo.json"), "w") as fh:
json.dump(options, fh, indent=2)
return stat_heter, heter_png, scope_txt, gse_txt, scope_png, gse_png, stat_genome, gc_depth