def filtervcf(args):
"""
%prog filtervcf NA12878.hg38.vcf.gz
Filter lobSTR VCF using script shipped in lobSTR. Input file can be a list
of vcf files.
"""
p = OptionParser(filtervcf.__doc__)
p.set_home("lobstr", default="/mnt/software/lobSTR")
p.set_aws_opts(store="hli-mv-data-science/htang/str")
p.set_cpus()
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
samples, = args
lhome = opts.lobstr_home
store = opts.output_path
if samples.endswith((".vcf", ".vcf.gz")):
vcffiles = [samples]
else:
vcffiles = [x.strip() for x in must_open(samples)]
vcffiles = [x for x in vcffiles if ".filtered." not in x]
run_args = [(x, lhome, x.startswith("s3://") and store) for x in vcffiles]
cpus = min(opts.cpus, len(run_args))
p = Pool(processes=cpus)
for res in p.map_async(run_filter, run_args).get():
continue
def filterdata(args):
"""
%prog filterdata data.bin samples.ids STR.ids allele_freq remove.ids final.ids
Filter subset of data after dropping remove.ids.
"""
p = OptionParser(filterdata.__doc__)
p.set_cpus()
opts, args = p.parse_args(args)
if len(args) != 6:
sys.exit(not p.print_help())
binfile, sampleids, strids, af, remove, final = args
df, m, samples, loci = read_binfile(binfile, sampleids, strids)
remove = [x.strip() for x in open(remove)]
removes = set(remove)
final = [x.strip() for x in open(final)]
assert len(loci) == len(remove) + len(final)
fp = open(af)
percentiles = {}
for row in fp:
sname, counts = row.split()
countsd = af_to_counts(counts)
percentile = counts_to_percentile(countsd)
percentiles[sname] = percentile
run_args = []
for i, sname in enumerate(loci):
if sname in removes:
continue
a = m[:, i]
percentile = percentiles[sname]
run_args.append((i, a, percentile))
cpus = min(opts.cpus, len(run_args))
p = Pool(processes=cpus)
res = []
for r in p.map_async(convert_to_percentile, run_args).get():
res.append(r)
res.sort()
# Write mask (P-value) matrix
ii, pvalues = zip(*res)
m = np.vstack(pvalues).T
write_csv("final.mask.tsv", m, samples, final)
df.drop(remove, inplace=True, axis=1)
df.columns = final
# Save a copy of the raw numpy array
filtered_bin = "filtered.bin"
m = df.as_matrix()
m[m < 0] = -1
m.tofile(filtered_bin)
logging.debug("Binary matrix written to `{}`".format(filtered_bin))
# Write data output
df.to_csv("final.data.tsv", sep="\t", index_label="SampleKey")
def filtervcf(args):
"""
%prog filtervcf NA12878.hg38.vcf.gz
Filter lobSTR VCF using script shipped in lobSTR. Input file can be a list
of vcf files.
"""
p = OptionParser(filtervcf.__doc__)
p.set_home("lobstr", default="/mnt/software/lobSTR")
p.set_aws_opts(store="hli-mv-data-science/htang/str")
p.set_cpus()
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
samples, = args
lhome = opts.lobstr_home
store = opts.output_path
if samples.endswith((".vcf", ".vcf.gz")):
vcffiles = [samples]
else:
vcffiles = [x.strip() for x in must_open(samples)]
vcffiles = [x for x in vcffiles if ".filtered." not in x]
run_args = [(x, lhome, x.startswith("s3://") and store) for x in vcffiles]
cpus = min(opts.cpus, len(run_args))
p = Pool(processes=cpus)
for res in p.map_async(run_filter, run_args).get():
continue
def filterdata(args):
"""
%prog filterdata data.bin samples.ids STR.ids allele_freq remove.ids final.ids
Filter subset of data after dropping remove.ids.
"""
p = OptionParser(filterdata.__doc__)
p.set_cpus()
opts, args = p.parse_args(args)
if len(args) != 6:
sys.exit(not p.print_help())
binfile, sampleids, strids, af, remove, final = args
df, m, samples, loci = read_binfile(binfile, sampleids, strids)
remove = [x.strip() for x in open(remove)]
removes = set(remove)
final = [x.strip() for x in open(final)]
assert len(loci) == len(remove) + len(final)
fp = open(af)
percentiles = {}
for row in fp:
sname, counts = row.split()
countsd = af_to_counts(counts)
percentile = counts_to_percentile(countsd)
percentiles[sname] = percentile
run_args = []
for i, sname in enumerate(loci):
if sname in removes:
continue
a = m[:, i]
percentile = percentiles[sname]
run_args.append((i, a, percentile))
cpus = min(opts.cpus, len(run_args))
p = Pool(processes=cpus)
res = []
for r in p.map_async(convert_to_percentile, run_args).get():
res.append(r)
res.sort()
# Write mask (P-value) matrix
ii, pvalues = zip(*res)
m = np.vstack(pvalues).T
write_csv("final.mask.tsv", m, samples, final)
df.drop(remove, inplace=True, axis=1)
df.columns = final
# Save a copy of the raw numpy array
filtered_bin = "filtered.bin"
m = df.as_matrix()
m[m < 0] = -1
m.tofile(filtered_bin)
logging.debug("Binary matrix written to `{}`".format(filtered_bin))
# Write data output
df.to_csv("final.data.tsv", sep="\t", index_label="SampleKey")
def compilevcf(args):
"""
%prog compilevcf samples.csv
Compile vcf results into master spreadsheet.
"""
p = OptionParser(compilevcf.__doc__)
p.add_option("--db", default="hg38", help="Use these lobSTR db")
p.add_option(
"--nofilter",
default=False,
action="store_true",
help="Do not filter the variants",
)
p.set_home("lobstr")
p.set_cpus()
p.set_aws_opts(store="hli-mv-data-science/htang/str-data")
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
(samples, ) = args
workdir = opts.workdir
store = opts.output_path
cleanup = not opts.nocleanup
filtered = not opts.nofilter
dbs = opts.db.split(",")
cwd = os.getcwd()
mkdir(workdir)
os.chdir(workdir)
samples = op.join(cwd, samples)
stridsfile = "STR.ids"
if samples.endswith((".vcf", ".vcf.gz")):
vcffiles = [samples]
else:
vcffiles = [x.strip() for x in must_open(samples)]
if not op.exists(stridsfile):
ids = []
for db in dbs:
ids.extend(STRFile(opts.lobstr_home, db=db).ids)
uids = uniqify(ids)
logging.debug("Combined: {} Unique: {}".format(len(ids), len(uids)))
fw = open(stridsfile, "w")
print("\n".join(uids), file=fw)
fw.close()
run_args = [(x, filtered, cleanup, store) for x in vcffiles]
cpus = min(opts.cpus, len(run_args))
p = Pool(processes=cpus)
for _ in p.map_async(run_compile, run_args).get():
continue
def compile(args):
"""
%prog compile samples.csv
Compile vcf results into master spreadsheet.
"""
from multiprocessing import Pool
p = OptionParser(compile.__doc__)
p.add_option("--db", default="hg38,hg38-named",
help="Use these lobSTR db")
p.set_home("lobstr")
p.set_cpus()
p.set_aws_opts(store="hli-mv-data-science/htang/str")
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
samples, = args
workdir = opts.workdir
dbs = opts.db.split(",")
mkdir(workdir)
os.chdir(workdir)
stridsfile = "STR.ids"
vcffiles = [x.strip() for x in must_open(samples)]
if not op.exists(stridsfile):
ids = []
for db in dbs:
ids.extend(STRFile(opts.lobstr_home, db=db).ids)
uids = uniqify(ids)
logging.debug("Combined: {} Unique: {}".format(len(ids), len(uids)))
fw = open(stridsfile, "w")
print >> fw, "\n".join(uids)
fw.close()
# Generate two alleles
dipuids = []
for uid in uids:
dipuids.extend([uid + ".1", uid + ".2"])
fw = open("header.ids", "w")
print >> fw, ",".join(dipuids)
fw.close()
p = Pool(processes=opts.cpus)
run_args = [(x, opts.store, opts.cleanup) for x in vcffiles]
#run(run_args[0])
for res in p.map_async(run, run_args).get():
continue
def compilevcf(args):
"""
%prog compilevcf samples.csv
Compile vcf results into master spreadsheet.
"""
p = OptionParser(compilevcf.__doc__)
p.add_option("--db", default="hg38", help="Use these lobSTR db")
p.add_option("--nofilter", default=False, action="store_true",
help="Do not filter the variants")
p.set_home("lobstr")
p.set_cpus()
p.set_aws_opts(store="hli-mv-data-science/htang/str-data")
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
samples, = args
workdir = opts.workdir
store = opts.output_path
cleanup = not opts.nocleanup
filtered = not opts.nofilter
dbs = opts.db.split(",")
cwd = os.getcwd()
mkdir(workdir)
os.chdir(workdir)
samples = op.join(cwd, samples)
stridsfile = "STR.ids"
if samples.endswith((".vcf", ".vcf.gz")):
vcffiles = [samples]
else:
vcffiles = [x.strip() for x in must_open(samples)]
if not op.exists(stridsfile):
ids = []
for db in dbs:
ids.extend(STRFile(opts.lobstr_home, db=db).ids)
uids = uniqify(ids)
logging.debug("Combined: {} Unique: {}".format(len(ids), len(uids)))
fw = open(stridsfile, "w")
print >> fw, "\n".join(uids)
fw.close()
run_args = [(x, filtered, cleanup, store) for x in vcffiles]
cpus = min(opts.cpus, len(run_args))
p = Pool(processes=cpus)
for res in p.map_async(run_compile, run_args).get():
continue
def compile(args):
"""
%prog compile samples.csv
Compile vcf results into master spreadsheet.
"""
p = OptionParser(compile.__doc__)
p.add_option("--db", default="hg38", help="Use these lobSTR db")
p.set_home("lobstr")
p.set_cpus()
p.set_aws_opts(store="hli-mv-data-science/htang/str-data")
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
samples, = args
workdir = opts.workdir
store = opts.output_path
cleanup = not opts.nocleanup
dbs = opts.db.split(",")
cwd = os.getcwd()
mkdir(workdir)
os.chdir(workdir)
samples = op.join(cwd, samples)
stridsfile = "STR.ids"
vcffiles = [x.strip() for x in must_open(samples)]
if not op.exists(stridsfile):
ids = []
for db in dbs:
ids.extend(STRFile(opts.lobstr_home, db=db).ids)
uids = uniqify(ids)
logging.debug("Combined: {} Unique: {}".format(len(ids), len(uids)))
fw = open(stridsfile, "w")
print >> fw, "\n".join(uids)
fw.close()
p = Pool(processes=opts.cpus)
run_args = [(x, store, cleanup) for x in vcffiles]
for res in p.map_async(run, run_args).get():
continue
def compare(args):
"""
%prog compare NA12878_array_hg38.bed *.seg
Compare cnv output to known ground truths.
"""
p = OptionParser(compare.__doc__)
p.set_cpus()
opts, args = p.parse_args(args)
if len(args) < 2:
sys.exit(not p.print_help())
truths = args[0]
cnvoutputs = args[1:]
cpus = min(len(cnvoutputs), opts.cpus)
p = Pool(processes=cpus)
results = []
files = [(x, truths) for x in cnvoutputs]
r = p.map_async(compare_worker, files, callback=results.append)
r.wait()
for res in results:
print("\n".join(res))
def compare(args):
"""
%prog compare NA12878_array_hg38.bed *.seg
Compare cnv output to known ground truths.
"""
p = OptionParser(compare.__doc__)
p.set_cpus()
opts, args = p.parse_args(args)
if len(args) < 2:
sys.exit(not p.print_help())
truths = args[0]
cnvoutputs = args[1:]
cpus = min(len(cnvoutputs), opts.cpus)
p = Pool(processes=cpus)
results = []
files = [(x, truths) for x in cnvoutputs]
r = p.map_async(compare_worker, files, callback=results.append)
r.wait()
for res in results:
print "\n".join(res)