def run_peddy(samples, out_dir=None):
vcf_file = None
for d in samples:
vcinfo = variant.get_active_vcinfo(d)
if vcinfo and vcinfo.get("vrn_file") and utils.file_exists(vcinfo["vrn_file"]):
if vcinfo["vrn_file"] and dd.get_sample_name(d) in vcfutils.get_samples(vcinfo["vrn_file"]):
vcf_file = vcinfo["vrn_file"]
break
data = samples[0]
peddy = config_utils.get_program("peddy", data) if config_utils.program_installed("peddy", data) else None
if not peddy or not vcf_file or not is_human(data):
logger.info("peddy is not installed, not human or sample VCFs don't match, skipping correspondence checking "
"for %s." % vcf_file)
return samples
batch = dd.get_batch(data) or dd.get_sample_name(data)
if out_dir:
peddy_dir = safe_makedir(out_dir)
else:
peddy_dir = safe_makedir(os.path.join(dd.get_work_dir(data), "qc", batch, "peddy"))
ped_file = create_ped_file(samples, vcf_file, out_dir=out_dir)
peddy_prefix = os.path.join(peddy_dir, batch)
peddy_report = peddy_prefix + ".html"
peddyfiles = expected_peddy_files(peddy_report, batch)
if file_exists(peddy_report):
return dd.set_in_samples(samples, dd.set_summary_qc, peddyfiles)
if file_exists(peddy_prefix + "-failed.log"):
return samples
num_cores = dd.get_num_cores(data)
with tx_tmpdir(data) as tx_dir:
peddy_prefix_tx = os.path.join(tx_dir, os.path.basename(peddy_prefix))
# Redirects stderr because incredibly noisy with no intervals found messages from cyvcf2
stderr_log = os.path.join(tx_dir, "run-stderr.log")
cmd = "{peddy} -p {num_cores} --plot --prefix {peddy_prefix_tx} {vcf_file} {ped_file} 2> {stderr_log}"
message = "Running peddy on {vcf_file} against {ped_file}."
try:
do.run(cmd.format(**locals()), message.format(**locals()))
except:
to_show = collections.deque(maxlen=100)
with open(stderr_log) as in_handle:
for line in in_handle:
to_show.append(line)
if any([l.find("IndexError") >=0 and l.find("is out of bounds for axis") >= 0
for l in to_show]):
logger.info("Skipping peddy because no variants overlap with checks: %s" % batch)
with open(peddy_prefix + "-failed.log", "w") as out_handle:
out_handle.write("peddy did not find overlaps with 1kg sites in VCF, skipping")
return samples
else:
logger.warning("".join(to_show))
raise
for ext in PEDDY_OUT_EXTENSIONS:
if os.path.exists(peddy_prefix_tx + ext):
shutil.move(peddy_prefix_tx + ext, peddy_prefix + ext)
return dd.set_in_samples(samples, dd.set_summary_qc, peddyfiles)
def run_peddy(samples, out_dir=None):
data = samples[0]
batch = dd.get_batch(data) or dd.get_sample_name(data)
if isinstance(batch, (list, tuple)):
batch = batch[0]
if out_dir:
peddy_dir = safe_makedir(out_dir)
else:
peddy_dir = safe_makedir(
os.path.join(dd.get_work_dir(data), "qc", batch, "peddy"))
peddy_prefix = os.path.join(peddy_dir, batch)
peddy_report = peddy_prefix + ".html"
vcf_file = None
for d in samples:
vcinfo = None
if dd.get_phenotype(d) == "germline" or dd.get_phenotype(d) not in [
"tumor"
]:
vcinfo = variant.get_active_vcinfo(d, use_ensemble=False)
if not vcinfo and dd.get_phenotype(d) in ["tumor"]:
vcinfo = variant.extract_germline_vcinfo(d, peddy_dir)
if vcinfo:
for key in ["germline", "vrn_file"]:
if vcinfo and vcinfo.get(key) and utils.file_exists(
vcinfo[key]):
if vcinfo[key] and dd.get_sample_name(
d) in vcfutils.get_samples(vcinfo[key]):
if vcinfo[
key] and vcfutils.vcf_has_nonfiltered_variants(
vcinfo[key]):
vcf_file = vcinfo[key]
break
peddy = config_utils.get_program("peddy",
data) if config_utils.program_installed(
"peddy", data) else None
config_skips = any(["peddy" in dd.get_tools_off(d) for d in samples])
if not peddy or not vcf_file or not vcfanno.is_human(data) or config_skips:
if not peddy:
reason = "peddy executable not found"
elif config_skips:
reason = "peddy in tools_off configuration"
elif not vcfanno.is_human(data):
reason = "sample is not human"
else:
assert not vcf_file
reason = "no suitable VCF files found with the sample and non-filtered variants"
msg = "Skipping peddy QC, %s: %s" % (
reason, [dd.get_sample_name(d) for d in samples])
with open(peddy_prefix + "-failed.log", "w") as out_handle:
out_handle.write(msg)
logger.info(msg)
return samples
if file_exists(peddy_prefix + "-failed.log"):
return samples
if not file_exists(peddy_report):
ped_file = create_ped_file(samples, vcf_file, out_dir=out_dir)
num_cores = dd.get_num_cores(data)
with tx_tmpdir(data) as tx_dir:
peddy_prefix_tx = os.path.join(tx_dir,
os.path.basename(peddy_prefix))
# Redirects stderr because incredibly noisy with no intervals found messages from cyvcf2
stderr_log = os.path.join(tx_dir, "run-stderr.log")
sites_str = "--sites hg38" if dd.get_genome_build(
data) == "hg38" else ""
locale = utils.locale_export()
cmd = (
"{locale} {peddy} -p {num_cores} {sites_str} --plot --prefix {peddy_prefix_tx} "
"{vcf_file} {ped_file} 2> {stderr_log}")
message = "Running peddy on {vcf_file} against {ped_file}."
try:
do.run(cmd.format(**locals()), message.format(**locals()))
except:
to_show = collections.deque(maxlen=100)
with open(stderr_log) as in_handle:
for line in in_handle:
to_show.append(line)
def allowed_errors(l):
return (
(l.find("IndexError") >= 0
and l.find("is out of bounds for axis") >= 0) or
(l.find("n_components=") >= 0
and l.find("must be between 1 and n_features=") >= 0)
or (l.find("n_components=") >= 0
and l.find("must be between 1 and min") >= 0)
or (l.find(
"Input contains NaN, infinity or a value too large for dtype"
) >= 0))
def all_line_errors(l):
return (l.find("no intervals found for") >= 0)
if any([allowed_errors(l) for l in to_show]) or all(
[all_line_errors(l) for l in to_show]):
logger.info(
"Skipping peddy because no variants overlap with checks: %s"
% batch)
with open(peddy_prefix + "-failed.log", "w") as out_handle:
out_handle.write(
"peddy did not find overlaps with 1kg sites in VCF, skipping"
)
return samples
else:
logger.warning("".join(to_show))
raise
for ext in PEDDY_OUT_EXTENSIONS:
if os.path.exists(peddy_prefix_tx + ext):
shutil.move(peddy_prefix_tx + ext, peddy_prefix + ext)
peddyfiles = expected_peddy_files(peddy_report, batch)
return dd.set_in_samples(samples, dd.set_summary_qc, peddyfiles)