def _run_purecn(paired, work_dir):
"""Run PureCN.R wrapper with pre-segmented CNVkit inputs.
"""
out_base, out, all_files = _get_purecn_files(paired, work_dir)
cnr_file = tz.get_in(["depth", "bins", "normalized"], paired.tumor_data)
if not utils.file_uptodate(out["rds"], cnr_file):
cnvkit_base = os.path.join(
utils.safe_makedir(os.path.join(work_dir, "cnvkit")),
dd.get_sample_name(paired.tumor_data))
seg_file = cnvkit.segment_from_cnr(cnr_file, paired.tumor_data,
cnvkit_base)
from bcbio import heterogeneity
vcf_file = heterogeneity.get_variants(paired.tumor_data)[0]["vrn_file"]
with file_transaction(paired.tumor_data, out_base) as tx_out_base:
cmd = [
"PureCN.R", "--seed", "42", "--out", tx_out_base, "--rds",
"%s.rds" % tx_out_base, "--sampleid",
dd.get_sample_name(paired.tumor_data), "--genome",
dd.get_genome_build(paired.tumor_data), "--vcf", vcf_file,
"--tumor", cnr_file, "--segfile", seg_file,
"--funsegmentation", "none"
]
do.run(cmd, "PureCN copy number calling")
for f in all_files:
shutil.move(os.path.join(os.path.dirname(tx_out_base), f),
os.path.join(os.path.dirname(out_base), f))
return out
def run(items):
from bcbio import heterogeneity
paired = vcfutils.get_paired(items)
if not paired:
logger.info("Skipping TitanCNA; no somatic tumor calls in batch: %s" %
" ".join([dd.get_sample_name(d) for d in items]))
return items
work_dir = _sv_workdir(paired.tumor_data)
cn_file = _titan_cn_file(dd.get_normalized_depth(paired.tumor_data),
work_dir, paired.tumor_data)
het_file = _titan_het_file(heterogeneity.get_variants(paired.tumor_data),
work_dir, paired)
if _should_run(het_file):
ploidy_outdirs = []
for ploidy in [2, 3, 4]:
for num_clusters in [1, 2, 3]:
out_dir = _run_titancna(cn_file, het_file, ploidy,
num_clusters, work_dir,
paired.tumor_data)
ploidy_outdirs.append((ploidy, out_dir))
solution_file = _run_select_solution(ploidy_outdirs, work_dir,
paired.tumor_data)
else:
logger.info("Skipping TitanCNA; not enough input data: %s" %
" ".join([dd.get_sample_name(d) for d in items]))
return items
out = []
if paired.normal_data:
out.append(paired.normal_data)
if "sv" not in paired.tumor_data:
paired.tumor_data["sv"] = []
paired.tumor_data["sv"].append(
_finalize_sv(solution_file, paired.tumor_data))
out.append(paired.tumor_data)
return out
def _run_purecn(paired, work_dir):
"""Run PureCN.R wrapper with pre-segmented CNVkit or GATK4 inputs.
"""
segfns = {"cnvkit": _segment_normalized_cnvkit, "gatk-cnv": _segment_normalized_gatk}
out_base, out, all_files = _get_purecn_files(paired, work_dir)
cnr_file = tz.get_in(["depth", "bins", "normalized"], paired.tumor_data)
if not utils.file_uptodate(out["rds"], cnr_file):
cnr_file, seg_file = segfns[cnvkit.bin_approach(paired.tumor_data)](cnr_file, work_dir, paired)
from bcbio import heterogeneity
vcf_file = heterogeneity.get_variants(paired.tumor_data, include_germline=False)[0]["vrn_file"]
vcf_file = germline.filter_to_pass_and_reject(vcf_file, paired, out_dir=work_dir)
with file_transaction(paired.tumor_data, out_base) as tx_out_base:
# Use UCSC style naming for human builds to support BSgenome
genome = ("hg19" if dd.get_genome_build(paired.tumor_data) in ["GRCh37", "hg19"]
else dd.get_genome_build(paired.tumor_data))
cmd = ["PureCN.R", "--seed", "42", "--out", tx_out_base, "--rds", "%s.rds" % tx_out_base,
"--sampleid", dd.get_sample_name(paired.tumor_data),
"--genome", genome,
"--vcf", vcf_file, "--tumor", cnr_file,
"--segfile", seg_file, "--funsegmentation", "Hclust", "--maxnonclonal", "0.3"]
if dd.get_num_cores(paired.tumor_data) > 1:
cmd += ["--cores", str(dd.get_num_cores(paired.tumor_data))]
do.run(cmd, "PureCN copy number calling")
for f in all_files:
shutil.move(os.path.join(os.path.dirname(tx_out_base), f),
os.path.join(os.path.dirname(out_base), f))
return out
def _run_purecn(paired, work_dir):
"""Run PureCN.R wrapper with pre-segmented CNVkit or GATK4 inputs.
"""
segfns = {
"cnvkit": _segment_normalized_cnvkit,
"gatk-cnv": _segment_normalized_gatk
}
out_base, out, all_files = _get_purecn_files(paired, work_dir)
failed_file = out_base + "-failed.log"
cnr_file = tz.get_in(["depth", "bins", "normalized"], paired.tumor_data)
if not utils.file_uptodate(
out["rds"], cnr_file) and not utils.file_exists(failed_file):
cnr_file, seg_file = segfns[cnvkit.bin_approach(paired.tumor_data)](
cnr_file, work_dir, paired)
from bcbio import heterogeneity
vcf_file = heterogeneity.get_variants(
paired.tumor_data, include_germline=False)[0]["vrn_file"]
vcf_file = germline.filter_to_pass_and_reject(vcf_file,
paired,
out_dir=work_dir)
with file_transaction(paired.tumor_data, out_base) as tx_out_base:
# Use UCSC style naming for human builds to support BSgenome
genome = ("hg19" if dd.get_genome_build(paired.tumor_data) in [
"GRCh37", "hg19"
] else dd.get_genome_build(paired.tumor_data))
cmd = [
"PureCN.R", "--seed", "42", "--out", tx_out_base, "--rds",
"%s.rds" % tx_out_base, "--sampleid",
dd.get_sample_name(paired.tumor_data), "--genome", genome,
"--vcf", vcf_file, "--tumor", cnr_file, "--segfile", seg_file,
"--funsegmentation", "Hclust", "--maxnonclonal", "0.3"
]
if dd.get_num_cores(paired.tumor_data) > 1:
cmd += ["--cores", str(dd.get_num_cores(paired.tumor_data))]
try:
cmd = "export R_LIBS_USER=%s && %s && %s" % (
utils.R_sitelib(), utils.get_R_exports(), " ".join(
[str(x) for x in cmd]))
do.run(cmd, "PureCN copy number calling")
except subprocess.CalledProcessError as msg:
if _allowed_errors(str(msg)):
logger.info(
"PureCN failed to find solution for %s: skipping" %
dd.get_sample_name(paired.tumor_data))
with open(failed_file, "w") as out_handle:
out_handle.write(str(msg))
else:
logger.exception()
raise
for f in all_files:
if os.path.exists(os.path.join(os.path.dirname(tx_out_base),
f)):
shutil.move(os.path.join(os.path.dirname(tx_out_base), f),
os.path.join(os.path.dirname(out_base), f))
out = _get_purecn_files(paired, work_dir, require_exist=True)[1]
return out if (out.get("rds") and os.path.exists(out["rds"])) else None
def run(items):
paired = vcfutils.get_paired(items)
if not paired or not paired.normal_name:
logger.info(
"Skipping PURPLE; need tumor/normal somatic calls in batch: %s" %
" ".join([dd.get_sample_name(d) for d in items]))
return items
work_dir = _sv_workdir(paired.tumor_data)
from bcbio import heterogeneity
het_file = _amber_het_file(heterogeneity.get_variants(paired.tumor_data),
work_dir, paired)
depth_file = _run_cobalt(paired, work_dir)
print(het_file, depth_file)
return items
def _compatible_small_variants(data, items):
"""Retrieve small variant (SNP, indel) VCFs compatible with CNVkit.
"""
from bcbio import heterogeneity
VarFile = collections.namedtuple("VarFile", ["name", "sample", "normal"])
out = []
paired = vcfutils.get_paired(items)
for v in heterogeneity.get_variants(data, include_germline=not paired):
vrn_file = v["vrn_file"]
base, ext = utils.splitext_plus(os.path.basename(vrn_file))
if paired:
out.append(VarFile(vrn_file, paired.tumor_name, paired.normal_name))
else:
out.append(VarFile(vrn_file, dd.get_sample_name(data), None))
return out
def _compatible_small_variants(data, items):
"""Retrieve small variant (SNP, indel) VCFs compatible with CNVkit.
"""
from bcbio import heterogeneity
VarFile = collections.namedtuple("VarFile", ["name", "sample", "normal"])
out = []
paired = vcfutils.get_paired(items)
for v in heterogeneity.get_variants(data, include_germline=not paired):
vrn_file = v["vrn_file"]
base, ext = utils.splitext_plus(os.path.basename(vrn_file))
if paired:
out.append(VarFile(vrn_file, paired.tumor_name, paired.normal_name))
else:
out.append(VarFile(vrn_file, dd.get_sample_name(data), None))
return out
def _run_purecn(paired, work_dir):
"""Run PureCN.R wrapper with pre-segmented CNVkit inputs.
"""
out_base, out, all_files = _get_purecn_files(paired, work_dir)
cnr_file = tz.get_in(["depth", "bins", "normalized"], paired.tumor_data)
if not utils.file_uptodate(out["rds"], cnr_file):
cnvkit_base = os.path.join(
utils.safe_makedir(os.path.join(work_dir, "cnvkit")),
dd.get_sample_name(paired.tumor_data))
cnr_file = chromhacks.bed_to_standardonly(
cnr_file,
paired.tumor_data,
headers="chromosome",
include_sex_chroms=True,
out_dir=os.path.dirname(cnvkit_base))
cnr_file = _remove_overlaps(cnr_file, os.path.dirname(cnvkit_base),
paired.tumor_data)
seg_file = cnvkit.segment_from_cnr(cnr_file, paired.tumor_data,
cnvkit_base)
from bcbio import heterogeneity
vcf_file = heterogeneity.get_variants(
paired.tumor_data, include_germline=False)[0]["vrn_file"]
vcf_file = germline.filter_to_pass_and_reject(vcf_file,
paired,
out_dir=work_dir)
with file_transaction(paired.tumor_data, out_base) as tx_out_base:
# Use UCSC style naming for human builds to support BSgenome
genome = ("hg19" if dd.get_genome_build(paired.tumor_data) in [
"GRCh37", "hg19"
] else dd.get_genome_build(paired.tumor_data))
cmd = [
"PureCN.R", "--seed", "42", "--out", tx_out_base, "--rds",
"%s.rds" % tx_out_base, "--sampleid",
dd.get_sample_name(paired.tumor_data), "--genome", genome,
"--vcf", vcf_file, "--tumor", cnr_file, "--segfile", seg_file,
"--funsegmentation", "Hclust", "--maxnonclonal", "0.3"
]
if dd.get_num_cores(paired.tumor_data) > 1:
cmd += ["--cores", str(dd.get_num_cores(paired.tumor_data))]
do.run(cmd, "PureCN copy number calling")
for f in all_files:
shutil.move(os.path.join(os.path.dirname(tx_out_base), f),
os.path.join(os.path.dirname(out_base), f))
return out
def _run_purecn(paired, work_dir):
"""Run PureCN.R wrapper with pre-segmented CNVkit or GATK4 inputs.
"""
segfns = {"cnvkit": _segment_normalized_cnvkit, "gatk-cnv": _segment_normalized_gatk}
out_base, out, all_files = _get_purecn_files(paired, work_dir)
failed_file = out_base + "-failed.log"
cnr_file = tz.get_in(["depth", "bins", "normalized"], paired.tumor_data)
if not utils.file_uptodate(out["rds"], cnr_file) and not utils.file_exists(failed_file):
cnr_file, seg_file = segfns[cnvkit.bin_approach(paired.tumor_data)](cnr_file, work_dir, paired)
from bcbio import heterogeneity
vcf_file = heterogeneity.get_variants(paired.tumor_data, include_germline=False)[0]["vrn_file"]
vcf_file = germline.filter_to_pass_and_reject(vcf_file, paired, out_dir=work_dir)
with file_transaction(paired.tumor_data, out_base) as tx_out_base:
# Use UCSC style naming for human builds to support BSgenome
genome = ("hg19" if dd.get_genome_build(paired.tumor_data) in ["GRCh37", "hg19"]
else dd.get_genome_build(paired.tumor_data))
cmd = ["PureCN.R", "--seed", "42", "--out", tx_out_base, "--rds", "%s.rds" % tx_out_base,
"--sampleid", dd.get_sample_name(paired.tumor_data),
"--genome", genome,
"--vcf", vcf_file, "--tumor", cnr_file,
"--segfile", seg_file, "--funsegmentation", "Hclust", "--maxnonclonal", "0.3"]
if dd.get_num_cores(paired.tumor_data) > 1:
cmd += ["--cores", str(dd.get_num_cores(paired.tumor_data))]
try:
cmd = "export R_LIBS_USER=%s && %s && %s" % (utils.R_sitelib(), utils.get_R_exports(),
" ".join([str(x) for x in cmd]))
do.run(cmd, "PureCN copy number calling")
except subprocess.CalledProcessError as msg:
if _allowed_errors(str(msg)):
logger.info("PureCN failed to find solution for %s: skipping" %
dd.get_sample_name(paired.tumor_data))
with open(failed_file, "w") as out_handle:
out_handle.write(str(msg))
else:
logger.exception()
raise
for f in all_files:
if os.path.exists(os.path.join(os.path.dirname(tx_out_base), f)):
shutil.move(os.path.join(os.path.dirname(tx_out_base), f),
os.path.join(os.path.dirname(out_base), f))
out = _get_purecn_files(paired, work_dir, require_exist=True)[1]
return out if (out.get("rds") and os.path.exists(out["rds"])) else None
def run(items):
paired = vcfutils.get_paired(items)
if not paired or not paired.normal_name:
logger.info("Skipping PURPLE; need tumor/normal somatic calls in batch: %s" %
" ".join([dd.get_sample_name(d) for d in items]))
return items
work_dir = _sv_workdir(paired.tumor_data)
from bcbio import heterogeneity
vrn_files = heterogeneity.get_variants(paired.tumor_data, include_germline=False)
het_file = _amber_het_file("pon", vrn_files, work_dir, paired)
depth_file = _run_cobalt(paired, work_dir)
purple_out = _run_purple(paired, het_file, depth_file, vrn_files, work_dir)
out = []
if paired.normal_data:
out.append(paired.normal_data)
if "sv" not in paired.tumor_data:
paired.tumor_data["sv"] = []
paired.tumor_data["sv"].append(purple_out)
out.append(paired.tumor_data)
return out
def run(items):
paired = vcfutils.get_paired(items)
if not paired or not paired.normal_name:
logger.info(
"Skipping PURPLE; need tumor/normal somatic calls in batch: %s" %
" ".join([dd.get_sample_name(d) for d in items]))
return items
work_dir = _sv_workdir(paired.tumor_data)
from bcbio import heterogeneity
vrn_files = heterogeneity.get_variants(paired.tumor_data,
include_germline=False)
het_file = _amber_het_file("pon", vrn_files, work_dir, paired)
depth_file = _run_cobalt(paired, work_dir)
purple_out = _run_purple(paired, het_file, depth_file, vrn_files, work_dir)
out = []
if paired.normal_data:
out.append(paired.normal_data)
if "sv" not in paired.tumor_data:
paired.tumor_data["sv"] = []
paired.tumor_data["sv"].append(purple_out)
out.append(paired.tumor_data)
return out
