def test_2_vcf_exclusion(self):
"""Exclude samples from VCF files.
"""
ref_file = os.path.join(self.data_dir, "genomes", "hg19", "seq", "hg19.fa")
config = load_config(os.path.join(self.data_dir, "automated",
"post_process-sample.yaml"))
out_file = utils.append_stem(self.combo_file, "-exclude")
to_exclude = ["S1"]
if os.path.exists(out_file):
os.remove(out_file)
vcfutils.exclude_samples(self.combo_file, out_file, to_exclude, ref_file, config)
def test_2_vcf_exclusion(self):
"""Exclude samples from VCF files.
"""
ref_file = os.path.join(self.data_dir, "genomes", "hg19", "seq", "hg19.fa")
with make_workdir() as workdir:
config = load_config(get_post_process_yaml(self.automated_dir, workdir))
config["algorithm"] = {}
out_file = utils.append_stem(self.combo_file, "-exclude")
to_exclude = ["S1"]
if os.path.exists(out_file):
os.remove(out_file)
vcfutils.exclude_samples(self.combo_file, out_file, to_exclude, ref_file, config)
def test_2_vcf_exclusion(self):
"""Exclude samples from VCF files.
"""
ref_file = os.path.join(self.data_dir, "genomes", "hg19", "seq", "hg19.fa")
with make_workdir() as workdir:
config = load_config(get_post_process_yaml(self.data_dir, workdir))
config["algorithm"] = {}
out_file = utils.append_stem(self.combo_file, "-exclude")
to_exclude = ["S1"]
if os.path.exists(out_file):
os.remove(out_file)
vcfutils.exclude_samples(self.combo_file, out_file, to_exclude, ref_file, config)
def test_2_vcf_exclusion(self):
"""Exclude samples from VCF files.
"""
fname = os.path.join(self.data_dir, "variants", "S1_S2-combined.vcf")
ref_file = os.path.join(self.data_dir, "genomes", "hg19", "seq", "hg19.fa")
config = load_config(os.path.join(self.data_dir, "automated",
"post_process-sample.yaml"))
out_file = "%s-exclude%s" % os.path.splitext(fname)
to_exclude = ["S1"]
if os.path.exists(out_file):
os.remove(out_file)
vcfutils.exclude_samples(fname, out_file, to_exclude, ref_file, config)
def test_2_vcf_exclusion(self, global_config):
"""Exclude samples from VCF files.
"""
from bcbio.variation import vcfutils
config = load_config(global_config)
config["algorithm"] = {}
out_file = utils.append_stem(self.combo_file, "-exclude")
to_exclude = ["S1"]
if os.path.exists(out_file):
os.remove(out_file)
vcfutils.exclude_samples(self.combo_file, out_file, to_exclude,
self.ref_file, config)
def test_2_vcf_exclusion(self):
"""Exclude samples from VCF files.
"""
with make_workdir() as workdir:
config = load_config(
get_post_process_yaml(self.automated_dir, workdir))
config["algorithm"] = {}
out_file = utils.append_stem(self.combo_file, "-exclude")
to_exclude = ["S1"]
if os.path.exists(out_file):
os.remove(out_file)
vcfutils.exclude_samples(self.combo_file, out_file, to_exclude,
self.ref_file, config)
def test_2_vcf_exclusion(self):
"""Exclude samples from VCF files.
"""
from bcbio.variation import vcfutils
with make_workdir() as workdir:
config = load_config(
get_post_process_yaml(self.automated_dir, workdir))
config["algorithm"] = {}
out_file = utils.append_stem(self.combo_file, "-exclude")
to_exclude = ["S1"]
if os.path.exists(out_file):
os.remove(out_file)
vcfutils.exclude_samples(
self.combo_file, out_file, to_exclude, self.ref_file, config)
def test_2_vcf_exclusion(self):
"""Exclude samples from VCF files.
"""
# Be back compatible with 0.7.6 -- remove after 0.7.7 release
if prun is None:
return
ref_file = os.path.join(self.data_dir, "genomes", "hg19", "seq", "hg19.fa")
config = load_config(os.path.join(self.data_dir, "automated",
"post_process-sample.yaml"))
out_file = utils.append_stem(self.combo_file, "-exclude")
to_exclude = ["S1"]
if os.path.exists(out_file):
os.remove(out_file)
vcfutils.exclude_samples(self.combo_file, out_file, to_exclude, ref_file, config)
def test_2_vcf_exclusion(self):
"""Exclude samples from VCF files.
"""
# Be back compatible with 0.7.6 -- remove after 0.7.7 release
if prun is None:
return
ref_file = os.path.join(self.data_dir, "genomes", "hg19", "seq", "hg19.fa")
with make_workdir() as workdir:
config = load_config(get_post_process_yaml(self.data_dir, workdir))
config["algorithm"] = {}
out_file = utils.append_stem(self.combo_file, "-exclude")
to_exclude = ["S1"]
if os.path.exists(out_file):
os.remove(out_file)
vcfutils.exclude_samples(self.combo_file, out_file, to_exclude, ref_file, config)
def main(config_file, env, cores):
cores = int(cores)
config = read_config(config_file, env)
idremap = read_remap_file(config["runinfo"]["idmapping"])
exclude = read_priority_file(config["runinfo"]["priority"], idremap)
samples = list(get_input_samples(config["inputs"], idremap))
problem = [x for x in samples if x["id"] is None]
if len(problem) > 0:
print "Problem identifiers"
for p in problem:
print p["illuminaid"], os.path.basename(p["dir"])
raise NotImplementedError
check_fam(samples, config["runinfo"]["fam"])
config["algorithm"] = {"num_cores": cores}
samples = [
s for s in samples if s["id"] is not None and s["id"] not in exclude
]
print "Processing %s samples" % len(samples)
out_files = [
outf for outf in joblib.Parallel(cores)(
joblib.delayed(run_illumina_prep)(s, config) for s in samples)
]
merge_file = merge_vcf_files(out_files, cores, config)
effects_file = effects.snpeff_effects({
"vrn_file": merge_file,
"sam_ref": config["ref"]["GRCh37"],
"reference": {
"fasta": {
"base": config["ref"]["GRCh37"]
}
},
"genome_resources": {
"aliases": {
"snpeff": "GRCh37.74"
}
},
"genome_build": "GRCh37",
"config": config
})
data = {"config": config, "dirs": {"work": os.getcwd()}, "name": [""]}
gemini_db = population.prep_gemini_db(
[os.path.join(os.getcwd(), effects_file)],
[utils.splitext_plus(config["outputs"]["merge"])[0], "casava", True],
[{
"config": config,
"work_bam": "yes",
"genome_build": "GRCh37",
"genome_resources": {
"aliases": {
"human": True
}
}
}], data)[0][1]["db"]
print gemini_db
noexclude_file = "%s-noexclude%s" % utils.splitext_plus(effects_file)
noexclude_file = vcfutils.exclude_samples(effects_file, noexclude_file,
exclude, config["ref"]["GRCh37"],
config)
prepare_plink_vcftools(noexclude_file, config)
def main(config_file, env, cores):
cores = int(cores)
config = read_config(config_file, env)
idremap = read_remap_file(config["runinfo"]["idmapping"])
exclude = read_priority_file(config["runinfo"]["priority"], idremap)
samples = list(get_input_samples(config["inputs"], idremap))
problem = [x for x in samples if x["id"] is None]
if len(problem) > 0:
print "Problem identifiers"
for p in problem:
print p["illuminaid"], os.path.basename(p["dir"])
raise NotImplementedError
check_fam(samples, config["runinfo"]["fam"])
config["algorithm"] = {"num_cores": cores}
samples = [s for s in samples if s["id"] is not None and s["id"] not in exclude]
print "Processing %s samples" % len(samples)
out_files = [outf for outf in joblib.Parallel(cores)(joblib.delayed(run_illumina_prep)(s, config)
for s in samples)]
merge_file = merge_vcf_files(out_files, cores, config)
effects_file = effects.snpeff_effects({"vrn_file": merge_file,
"sam_ref": config["ref"]["GRCh37"],
"reference": {"fasta" : {"base": config["ref"]["GRCh37"]}},
"genome_resources": {"aliases" : {"snpeff": "GRCh37.74"}},
"genome_build": "GRCh37",
"config": config})
data = {"config": config, "dirs": {"work": os.getcwd()}, "name": [""]}
gemini_db = population.prep_gemini_db([os.path.join(os.getcwd(), effects_file)],
[utils.splitext_plus(config["outputs"]["merge"])[0], "casava", True],
[{"config": config, "work_bam": "yes", "genome_build": "GRCh37",
"genome_resources": {"aliases": {"human": True}}}],
data)[0][1]["db"]
print gemini_db
noexclude_file = "%s-noexclude%s" % utils.splitext_plus(effects_file)
noexclude_file = vcfutils.exclude_samples(effects_file, noexclude_file, exclude,
config["ref"]["GRCh37"], config)
prepare_plink_vcftools(noexclude_file, config)
