def main(args):
options = parse_args(args)
RealTimeLogger.start_master()
filtered_gams = []
skip_words = options.skip.split(",")
for gam in options.in_gams:
skip_gam = False
for word in skip_words:
if len(word) > 0 and word in gam:
skip_gam = True
if not skip_gam:
filtered_gams.append(gam)
options.in_gams = filtered_gams
for gam in options.in_gams:
if len(gam.split("/")) < 3 or os.path.splitext(gam)[1] != ".gam":
raise RuntimeError("Input gam paths must be of the form "
".../<alg>/<reads>/<filename>.gam")
# Make a root job
root_job = Job.wrapJobFn(call_variants, options,
cores=1, memory="2G", disk="2G")
# Run it and see how many jobs fail
failed_jobs = Job.Runner.startToil(root_job, options)
if failed_jobs > 0:
raise Exception("{} jobs failed!".format(failed_jobs))
RealTimeLogger.stop_master()
def main(args):
options = parse_args(args)
RealTimeLogger.start_master()
filtered_gams = []
skip_words = options.skip.split(",")
for gam in options.in_gams:
skip_gam = False
for word in skip_words:
if len(word) > 0 and word in gam:
skip_gam = True
if not skip_gam:
filtered_gams.append(gam)
options.in_gams = filtered_gams
for gam in options.in_gams:
if len(gam.split("/")) < 3 or os.path.splitext(gam)[1] != ".gam":
raise RuntimeError("Input gam paths must be of the form "
".../<alg>/<reads>/<filename>.gam")
# Make a root job
root_job = Job.wrapJobFn(call_variants, options,
cores=1, memory="2G", disk="2G")
# Run it and see how many jobs fail
failed_jobs = Job.Runner.startToil(root_job, options)
if failed_jobs > 0:
raise Exception("{} jobs failed!".format(failed_jobs))
RealTimeLogger.stop_master()
def main(args):
options = parse_args(args)
RealTimeLogger.start_master()
for gam in options.in_gams:
if len(gam.split("/")) < 3 or os.path.splitext(gam)[1] != ".gam":
raise RuntimeError("Input gam paths must be of the form "
".../<alg>/<reads>/<filename>.gam")
robust_makedirs(json_out_path(options))
robust_makedirs(compare_out_path(options))
# Make a root job
root_job = Job.wrapJobFn(compute_all_indexes, options,
cores=1, memory="2G", disk=0)
# Run it and see how many jobs fail
if not options.only_summary:
failed_jobs = Job.Runner.startToil(root_job, options)
else:
failed_jobs = 0
if failed_jobs > 0:
raise Exception("{} jobs failed!".format(failed_jobs))
RealTimeLogger.stop_master()
# make some tables from the json comparison output
#dist_table(options)
#acc_table(options)
snp_count_table(options)
graph_size_table(options)
def main(args):
options = parse_args(args)
RealTimeLogger.start_master()
for graph in options.graphs:
if os.path.splitext(graph)[1] != ".vg":
raise RuntimeError("Input graphs expected to have .vg extension")
# Make a root job
root_job = Job.wrapJobFn(compute_kmer_indexes, options,
cores=1, memory="2G", disk=0)
# Run it and see how many jobs fail
if not options.only_summary:
failed_jobs = Job.Runner.startToil(root_job, options)
else:
failed_jobs = 0
if failed_jobs > 0:
raise Exception("{} jobs failed!".format(failed_jobs))
RealTimeLogger.stop_master()
# Do the drawing outside toil to get around weird import problems
cluster_comparisons(options)
def main(args):
options = parse_args(args)
RealTimeLogger.start_master()
robust_makedirs(options.out_dir)
vcfmap = munge_vcf_results(options.comp_dir)
mergetable = make_trio_vcfs(vcfmap, options)
do_mendel(mergetable, options)
def main(args):
options = parse_args(args)
RealTimeLogger.start_master()
robust_makedirs(options.out_dir)
vcfmap = munge_vcf_results(options.comp_dir)
mergetable = make_trio_vcfs(vcfmap, options)
do_mendel(mergetable, options)
def main(args):
options = parse_args(args)
RealTimeLogger.start_master()
# Make a root job
root_job = Job.wrapJobFn(run_and_evaluate, options,
cores=1, memory="2G", disk="2G")
# Run it and get the return value
answer = Job.Runner.startToil(root_job, options)
RealTimeLogger.stop_master()
print("Root return value:")
print(answer)
def main(args):
options = parse_args(args)
RealTimeLogger.start_master()
if options.classic:
# expect call_dir/SAMPLE/region.vcf
for sampledir in glob.glob(os.path.join(options.call_dir, "*")):
if os.path.isdir(sampledir):
sample = os.path.basename(sampledir)
vcfs = []
outfile = os.path.join(sampledir, "TOTAL.vcf")
for vcf in glob.glob(os.path.join(sampledir, "*.vcf")):
if os.path.basename(vcf) in ["BRCA1.vcf", "BRCA2.vcf", "SMA.vcf", "LRC_KIR.vcf", "MHC.vcf"]:
run("vcfsort {} > {}.sort".format(vcf, vcf), fail_hard = True)
run("bgzip -c {}.sort > {}.gz".format(vcf, vcf), fail_hard = True)
run("rm -f {}.sort".format(vcf))
run("tabix -f -p vcf {}.gz".format(vcf), fail_hard = True)
vcfs.append("{}.gz".format(vcf))
if len(vcfs) > 0:
run("vt cat {} > {}".format(" ".join(vcfs), outfile),
fail_hard = True)
run("vcfsort {} > {}.sort".format(outfile, outfile), fail_hard = True)
run("mv {}.sort {}".format(outfile, outfile), fail_hard = True)
run("bgzip -c {} > {}.gz".format(outfile, outfile), fail_hard = True)
run("tabix -f -p vcf {}.gz".format(outfile), fail_hard = True)
return 0
# expect call_dir/<REGION>/<GRAPH>/<SAMPLE>_sample.vcf
# count up regions
regions = set()
for regiondir in glob.glob(os.path.join(options.call_dir, "*")):
if os.path.isdir(regiondir):
region = os.path.basename(regiondir)
# avoid crufty directories (including outputs of previous runs of this script)
if region in ["brca1", "brca2", "mhc", "lrc_kir", "sma"]:
regions.add(region)
print regions
# count up graphs (that are present in every region)
graphs = set()
gcount = defaultdict(int)
for region in regions:
for graphdir in glob.glob(os.path.join(options.call_dir, region, "*")):
if os.path.isdir(graphdir):
graph = os.path.basename(graphdir)
gcount[graph] = gcount[graph] + 1
for graph, count in gcount.items():
if count == len(regions):
graphs.add(graph)
print graphs
# count up samples
samples = set()
scount = defaultdict(int)
for region in regions:
for graph in graphs:
for vcf in glob.glob(os.path.join(options.call_dir, region, graph, "*_sample.vcf")):
sample = os.path.basename(vcf).split("_")[0]
scount[sample] = scount[sample] + 1
for sample, count in scount.items():
samples.add(sample)
print samples
# make our output directory
out_dir = os.path.join(options.call_dir, options.name)
robust_makedirs(out_dir)
for graph in graphs:
g_out_dir = os.path.join(out_dir, graph)
for sample in samples:
vcf_files = []
for region in regions:
vcf = os.path.join(options.call_dir, region, graph, "{}_sample.vcf".format(sample))
if os.path.isfile(vcf):
vcf_files.append((region, vcf))
# this sample doesn't span all regions, skip it
if len(vcf_files) < len(regions):
print "Skipping Sample {} for Graph {}".format(sample, graph)
continue
# output vcf
merge_vcf_path = os.path.join(out_dir, graph, "{}_sample.vcf".format(sample))
# working directory for intermediates / debugging
work_path = os.path.join(out_dir, graph, "input", sample)
robust_makedirs(work_path)
# preprocess all the vcfs and leave in input dir
input_files = []
for region, vcf in vcf_files:
outbase = os.path.join(work_path, region)
run("vcfsort {} > {}.vcf".format(vcf, outbase), fail_hard = True)
run("bgzip -f {}.vcf".format(outbase))
run("tabix -f -p vcf {}.vcf.gz".format(outbase))
input_files.append("{}.vcf.gz".format(outbase))
# run the merge
run("vt cat {} > {}".format(" ".join(input_files), merge_vcf_path), fail_hard = True)
# make an index just in case
run("vcfsort {} > {}.sort".format(merge_vcf_path, merge_vcf_path), fail_hard = True)
run("mv {}.sort {}".format(merge_vcf_path, merge_vcf_path), fail_hard = True)
run("bgzip -c {} > {}.gz".format(merge_vcf_path, merge_vcf_path), fail_hard = True)
run("tabix -f -p vcf {}.gz".format(merge_vcf_path, merge_vcf_path), fail_hard = True)
return 0
def main(args):
options = parse_args(args)
RealTimeLogger.start_master()
if options.classic:
# expect call_dir/SAMPLE/region.vcf
for sampledir in glob.glob(os.path.join(options.call_dir, "*")):
if os.path.isdir(sampledir):
sample = os.path.basename(sampledir)
vcfs = []
outfile = os.path.join(sampledir, "TOTAL.vcf")
for vcf in glob.glob(os.path.join(sampledir, "*.vcf")):
if os.path.basename(vcf) in [
"BRCA1.vcf", "BRCA2.vcf", "SMA.vcf", "LRC_KIR.vcf",
"MHC.vcf"
]:
run("vcfsort {} > {}.sort".format(vcf, vcf),
fail_hard=True)
run("bgzip -c {}.sort > {}.gz".format(vcf, vcf),
fail_hard=True)
run("rm -f {}.sort".format(vcf))
run("tabix -f -p vcf {}.gz".format(vcf),
fail_hard=True)
vcfs.append("{}.gz".format(vcf))
if len(vcfs) > 0:
run("vt cat {} > {}".format(" ".join(vcfs), outfile),
fail_hard=True)
run("vcfsort {} > {}.sort".format(outfile, outfile),
fail_hard=True)
run("mv {}.sort {}".format(outfile, outfile),
fail_hard=True)
run("bgzip -c {} > {}.gz".format(outfile, outfile),
fail_hard=True)
run("tabix -f -p vcf {}.gz".format(outfile),
fail_hard=True)
return 0
# expect call_dir/<REGION>/<GRAPH>/<SAMPLE>_sample.vcf
# count up regions
regions = set()
for regiondir in glob.glob(os.path.join(options.call_dir, "*")):
if os.path.isdir(regiondir):
region = os.path.basename(regiondir)
# avoid crufty directories (including outputs of previous runs of this script)
if region in ["brca1", "brca2", "mhc", "lrc_kir", "sma"]:
regions.add(region)
print regions
# count up graphs (that are present in every region)
graphs = set()
gcount = defaultdict(int)
for region in regions:
for graphdir in glob.glob(os.path.join(options.call_dir, region, "*")):
if os.path.isdir(graphdir):
graph = os.path.basename(graphdir)
gcount[graph] = gcount[graph] + 1
for graph, count in gcount.items():
if count == len(regions):
graphs.add(graph)
print graphs
# count up samples
samples = set()
scount = defaultdict(int)
for region in regions:
for graph in graphs:
for vcf in glob.glob(
os.path.join(options.call_dir, region, graph,
"*_sample.vcf")):
sample = os.path.basename(vcf).split("_")[0]
scount[sample] = scount[sample] + 1
for sample, count in scount.items():
samples.add(sample)
print samples
# make our output directory
out_dir = os.path.join(options.call_dir, options.name)
robust_makedirs(out_dir)
for graph in graphs:
g_out_dir = os.path.join(out_dir, graph)
for sample in samples:
vcf_files = []
for region in regions:
vcf = os.path.join(options.call_dir, region, graph,
"{}_sample.vcf".format(sample))
if os.path.isfile(vcf):
vcf_files.append((region, vcf))
# this sample doesn't span all regions, skip it
if len(vcf_files) < len(regions):
print "Skipping Sample {} for Graph {}".format(sample, graph)
continue
# output vcf
merge_vcf_path = os.path.join(out_dir, graph,
"{}_sample.vcf".format(sample))
# working directory for intermediates / debugging
work_path = os.path.join(out_dir, graph, "input", sample)
robust_makedirs(work_path)
# preprocess all the vcfs and leave in input dir
input_files = []
for region, vcf in vcf_files:
outbase = os.path.join(work_path, region)
run("vcfsort {} > {}.vcf".format(vcf, outbase), fail_hard=True)
run("bgzip -f {}.vcf".format(outbase))
run("tabix -f -p vcf {}.vcf.gz".format(outbase))
input_files.append("{}.vcf.gz".format(outbase))
# run the merge
run("vt cat {} > {}".format(" ".join(input_files), merge_vcf_path),
fail_hard=True)
# make an index just in case
run("vcfsort {} > {}.sort".format(merge_vcf_path, merge_vcf_path),
fail_hard=True)
run("mv {}.sort {}".format(merge_vcf_path, merge_vcf_path),
fail_hard=True)
run("bgzip -c {} > {}.gz".format(merge_vcf_path, merge_vcf_path),
fail_hard=True)
run("tabix -f -p vcf {}.gz".format(merge_vcf_path, merge_vcf_path),
fail_hard=True)
return 0
