def test_programs(self):
"""Identify programs and versions used in analysis.
"""
with make_workdir() as workdir:
config = load_config(
get_post_process_yaml(self.automated_dir, workdir))
print programs._get_versions(config)
def test_1_parallel_vcf_combine(self):
"""Parallel combination of VCF files, split by chromosome.
"""
files = [
os.path.join(self.var_dir, "S1-variants.vcf"),
os.path.join(self.var_dir, "S2-variants.vcf")
]
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"] = {}
region_dir = os.path.join(self.var_dir, "S1_S2-combined-regions")
if os.path.exists(region_dir):
shutil.rmtree(region_dir)
if os.path.exists(self.combo_file):
os.remove(self.combo_file)
with prun.start({
"type": "local",
"cores": 1
}, [[config]], config) as run_parallel:
vcfutils.parallel_combine_variants(files, self.combo_file,
ref_file, config, run_parallel)
for fname in files:
if os.path.exists(fname + ".gz"):
subprocess.check_call(["gunzip", fname + ".gz"])
if os.path.exists(fname + ".gz.tbi"):
os.remove(fname + ".gz.tbi")
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 setUp(self):
make_workdir()
# Make up some barcode numbers
self.workdir = os.path.join(os.path.dirname(__file__), "test_automated_output")
self.data_dir = os.path.join(os.path.dirname(__file__), "data", "automated")
# Parse the run_info
run_info_file = os.path.join(self.data_dir, "run_info-gdocs.yaml")
with open(run_info_file) as fh:
self.run_info = yaml.load(fh)
# Make up bogus run names
self.runname = ("111014_SN0000_0001_AB0AAAACXX","111014_SN0000_0002_BB0AAAACXX")
# Create the run directories (create them if necessary)
for name in self.runname:
analysisdir = os.path.join(self.workdir, name)
if os.path.exists(analysisdir):
shutil.rmtree(analysisdir)
os.makedirs(analysisdir)
self._make_bc_metrics(name,analysisdir)
def setUp(self):
make_workdir()
# Make up some barcode numbers
self.workdir = os.path.join(os.path.dirname(__file__), "test_automated_output")
self.data_dir = os.path.join(os.path.dirname(__file__), "data", "automated")
# Parse the run_info
self.run_info_file = os.path.join(self.data_dir, "run_info-gdocs.yaml")
with open(self.run_info_file) as fh:
self.run_info = yaml.load(fh)
# Make up bogus run names
self.runname = ("111014_SN0000_0001_AB0AAAACXX", "111014_SN0000_0002_BB0AAAACXX")
# Create the run directories (create them if necessary)
for name in self.runname:
analysisdir = os.path.join(self.workdir, name)
if os.path.exists(analysisdir):
shutil.rmtree(analysisdir)
os.makedirs(analysisdir)
self._make_bc_metrics(name, analysisdir)
self._make_qc_metrics(name, analysisdir)
def test_3_vcf_split_combine(self):
"""Split a VCF file into SNPs and indels, then combine back together.
"""
with make_workdir() as workdir:
config = load_config(get_post_process_yaml(self.automated_dir, workdir))
config["algorithm"] = {}
ref_file = os.path.join(self.data_dir, "genomes", "hg19", "seq", "hg19.fa")
fname = os.path.join(self.var_dir, "S1-variants.vcf")
snp_file, indel_file = vcfutils.split_snps_indels(fname, ref_file, config)
merge_file = "%s-merge%s.gz" % os.path.splitext(fname)
vcfutils.combine_variant_files([snp_file, indel_file], merge_file, ref_file,
config)
for f in [snp_file, indel_file, merge_file]:
self._remove_vcf(f)
def test_3_vcf_split_combine(self):
"""Split a VCF file into SNPs and indels, then combine back together.
"""
with make_workdir() as workdir:
config = load_config(get_post_process_yaml(self.data_dir, workdir))
config["algorithm"] = {}
ref_file = os.path.join(self.data_dir, "genomes", "hg19", "seq", "hg19.fa")
fname = os.path.join(self.var_dir, "S1-variants.vcf")
snp_file, indel_file = vcfutils.split_snps_indels(fname, ref_file, config)
merge_file = "%s-merge%s.gz" % os.path.splitext(fname)
vcfutils.combine_variant_files([snp_file, indel_file], merge_file, ref_file,
config)
for f in [snp_file, indel_file, merge_file]:
self._remove_vcf(f)
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 test_1_parallel_vcf_combine(self):
"""Parallel combination of VCF files, split by chromosome.
"""
files = [os.path.join(self.var_dir, "S1-variants.vcf"), os.path.join(self.var_dir, "S2-variants.vcf")]
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"] = {}
region_dir = os.path.join(self.var_dir, "S1_S2-combined-regions")
if os.path.exists(region_dir):
shutil.rmtree(region_dir)
if os.path.exists(self.combo_file):
os.remove(self.combo_file)
with prun.start({"type": "local", "cores": 1}, [[config]], config) as run_parallel:
vcfutils.parallel_combine_variants(files, self.combo_file, ref_file, config, run_parallel)
for fname in files:
if os.path.exists(fname + ".gz"):
subprocess.check_call(["gunzip", fname + ".gz"])
if os.path.exists(fname + ".gz.tbi"):
os.remove(fname + ".gz.tbi")
def test_programs(self):
"""Identify programs and versions used in analysis.
"""
with make_workdir() as workdir:
config = load_config(get_post_process_yaml(self.data_dir, workdir))
print programs._get_versions(config)
