def _add_bed_to_output(out, data):
"""Call ploidy and convert into BED representation.
"""
call_file = "%s-call%s" % os.path.splitext(out["cns"])
gender = dd.get_gender(data)
if not utils.file_exists(call_file):
with file_transaction(data, call_file) as tx_call_file:
cmd = [os.path.join(os.path.dirname(sys.executable), "cnvkit.py"), "call",
"--ploidy", str(dd.get_ploidy(data)),
"-o", tx_call_file, out["cns"]]
if gender:
cmd += ["--gender", gender]
if gender.lower() == "male":
cmd += ["--male-reference"]
do.run(cmd, "CNVkit call ploidy")
out_file = "%s.bed" % os.path.splitext(call_file)[0]
if not utils.file_exists(out_file):
with file_transaction(data, out_file) as tx_out_file:
cmd = [os.path.join(os.path.dirname(sys.executable), "cnvkit.py"), "export",
"bed", "--sample-id", dd.get_sample_name(data),
"--ploidy", str(dd.get_ploidy(data)),
"-o", tx_out_file, call_file]
if gender and gender.lower() == "male":
cmd += ["--male-reference"]
do.run(cmd, "CNVkit export BED")
out["call_file"] = call_file
out["vrn_file"] = annotate.add_genes(out_file, data)
return out
def _add_variantcalls_to_output(out, data):
"""Call ploidy and convert into VCF and BED representations.
"""
call_file = "%s-call%s" % os.path.splitext(out["cns"])
gender = dd.get_gender(data)
if not utils.file_exists(call_file):
with file_transaction(data, call_file) as tx_call_file:
cmd = [os.path.join(os.path.dirname(sys.executable), "cnvkit.py"), "call",
"--ploidy", str(dd.get_ploidy(data)),
"-o", tx_call_file, out["cns"]]
if gender:
cmd += ["--gender", gender]
if gender.lower() == "male":
cmd += ["--male-reference"]
do.run(cmd, "CNVkit call ploidy")
calls = {}
for outformat in ["bed", "vcf"]:
out_file = "%s.%s" % (os.path.splitext(call_file)[0], outformat)
calls[outformat] = out_file
if not utils.file_exists(out_file):
with file_transaction(data, out_file) as tx_out_file:
cmd = [os.path.join(os.path.dirname(sys.executable), "cnvkit.py"), "export",
outformat, "--sample-id", dd.get_sample_name(data),
"--ploidy", str(dd.get_ploidy(data)),
"-o", tx_out_file, call_file]
if gender and gender.lower() == "male":
cmd += ["--male-reference"]
do.run(cmd, "CNVkit export %s" % outformat)
out["call_file"] = call_file
out["vrn_bed"] = annotate.add_genes(calls["bed"], data)
effects_vcf, _ = effects.add_to_vcf(calls["vcf"], data, "snpeff")
out["vrn_file"] = effects_vcf or calls["vcf"]
return out
def _code_gender(data):
g = dd.get_gender(data)
if g and g.lower() == "male":
return 1
elif g and g.lower() == "female":
return 2
else:
return 0
def _code_gender(data):
g = dd.get_gender(data)
if g and g.lower() == "male":
return 1
elif g and g.lower() == "female":
return 2
else:
return 0
def _code_gender(data):
g = dd.get_gender(data)
if g and str(g).lower() in ["male", "m"]:
return 1
elif g and str(g).lower() in ["female", "f"]:
return 2
else:
return 0
def _code_gender(data):
g = dd.get_gender(data)
if g and str(g).lower() in ["male", "m"]:
return 1
elif g and str(g).lower() in ["female", "f"]:
return 2
else:
return 0
def get_gender(data):
"""Retrieve gender from metadata, codified as male/female/unknown.
"""
g = str(dd.get_gender(data))
if g and str(g).lower() in ["male", "m", "1"]:
return "male"
elif g and str(g).lower() in ["female", "f", "2"]:
return "female"
else:
return "unknown"
def _add_diagram_plot(out, data):
out_file = "%s-diagram.pdf" % os.path.splitext(out["cnr"])[0]
cnr = _remove_haplotype_chroms(out["cnr"], data)
cns = _remove_haplotype_chroms(out["cns"], data)
if not utils.file_exists(out_file):
with file_transaction(data, out_file) as tx_out_file:
cmd = [_get_cmd(), "diagram", "-s", cns,
"-o", tx_out_file, cnr]
gender = dd.get_gender(data)
if gender and gender.lower() == "male":
cmd += ["--male-reference"]
do.run(cmd, "CNVkit diagram plot")
return out_file
def _add_diagram_plot(out, data):
out_file = "%s-diagram.pdf" % os.path.splitext(out["cnr"])[0]
cnr = _remove_haplotype_chroms(out["cnr"], data)
cns = _remove_haplotype_chroms(out["cns"], data)
if _cnx_is_empty(cnr) or _cnx_is_empty(cns):
return None
if not utils.file_exists(out_file):
with file_transaction(data, out_file) as tx_out_file:
cmd = [_get_cmd(), "diagram", "-s", cns, "-o", tx_out_file, cnr]
gender = dd.get_gender(data)
if gender and gender.lower() == "male":
cmd += ["--male-reference"]
do.run(cmd, "CNVkit diagram plot")
return out_file
def _add_bed_to_output(out, data):
"""Add FreeBayes cnvmap BED-like representation to the output.
"""
out_file = "%s.bed" % os.path.splitext(out["cns"])[0]
if not utils.file_exists(out_file):
with file_transaction(data, out_file) as tx_out_file:
cmd = [os.path.join(os.path.dirname(sys.executable), "cnvkit.py"), "export",
"freebayes", "--name", dd.get_sample_name(data),
"--ploidy", str(dd.get_ploidy(data)),
"-o", tx_out_file, out["cns"]]
gender = dd.get_gender(data)
if gender:
cmd += ["--gender", gender]
do.run(cmd, "CNVkit export FreeBayes BED cnvmap")
out["vrn_file"] = out_file
return out
def _add_bed_to_output(out, data):
"""Add FreeBayes cnvmap BED-like representation to the output.
"""
out_file = "%s.bed" % os.path.splitext(out["cns"])[0]
if not utils.file_exists(out_file):
with file_transaction(data, out_file) as tx_out_file:
cmd = [os.path.join(os.path.dirname(sys.executable), "cnvkit.py"), "export",
"freebayes", "--name", dd.get_sample_name(data),
"--ploidy", str(dd.get_ploidy(data)),
"-o", tx_out_file, out["cns"]]
gender = dd.get_gender(data)
if gender:
cmd += ["--gender", gender]
do.run(cmd, "CNVkit export FreeBayes BED cnvmap")
out["vrn_file"] = out_file
return out
def _add_variantcalls_to_output(out, data):
"""Call ploidy and convert into VCF and BED representations.
"""
call_file = "%s-call%s" % os.path.splitext(out["cns"])
gender = dd.get_gender(data)
if not utils.file_exists(call_file):
with file_transaction(data, call_file) as tx_call_file:
cmd = [
os.path.join(os.path.dirname(sys.executable), "cnvkit.py"),
"call", "--ploidy",
str(dd.get_ploidy(data)), "-o", tx_call_file, out["cns"]
]
if gender:
cmd += ["--gender", gender]
if gender.lower() == "male":
cmd += ["--male-reference"]
do.run(cmd, "CNVkit call ploidy")
calls = {}
for outformat in ["bed", "vcf"]:
out_file = "%s.%s" % (os.path.splitext(call_file)[0], outformat)
calls[outformat] = out_file
if not utils.file_exists(out_file):
with file_transaction(data, out_file) as tx_out_file:
cmd = [
os.path.join(os.path.dirname(sys.executable), "cnvkit.py"),
"export", outformat, "--sample-id",
dd.get_sample_name(data), "--ploidy",
str(dd.get_ploidy(data)), "-o", tx_out_file, call_file
]
if gender and gender.lower() == "male":
cmd += ["--male-reference"]
do.run(cmd, "CNVkit export %s" % outformat)
out["call_file"] = call_file
out["vrn_bed"] = annotate.add_genes(calls["bed"], data)
effects_vcf, _ = effects.add_to_vcf(calls["vcf"], data, "snpeff")
out["vrn_file"] = effects_vcf or calls["vcf"]
return out
