def test_1_parallel_vcf_combine(self): """Parallel combination of VCF files, split by chromosome. """ var_dir = os.path.join(self.data_dir, "variants") files = [ os.path.join(var_dir, "S1-variants.vcf"), os.path.join(var_dir, "S2-variants.vcf") ] out_file = os.path.join(var_dir, "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")) run_parallel = parallel_runner({ "type": "local", "cores": 1 }, {}, config) region_dir = os.path.join(var_dir, "S1_S2-combined-regions") if os.path.exists(region_dir): shutil.rmtree(region_dir) if os.path.exists(out_file): os.remove(out_file) vcfutils.parallel_combine_variants(files, out_file, ref_file, config, run_parallel)
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_1_parallel_vcf_combine(self, global_config): """Parallel combination of VCF files, split by chromosome. """ from bcbio.variation import vcfutils files = [ os.path.join(self.var_dir, "S1-variants.vcf"), os.path.join(self.var_dir, "S2-variants.vcf") ] config = load_config(global_config) 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) reqs = {"type": "local", "cores": 1} with prun.start(reqs, [[config]], config) as run_parallel: vcfutils.parallel_combine_variants(files, self.combo_file, self.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_1_parallel_vcf_combine(self): """Parallel combination of VCF files, split by chromosome. """ from bcbio.variation import vcfutils files = [ os.path.join(self.var_dir, "S1-variants.vcf"), os.path.join(self.var_dir, "S2-variants.vcf") ] 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) reqs = {"type": "local", "cores": 1} with prun.start(reqs, [[config]], config) as run_parallel: vcfutils.parallel_combine_variants( files, self.combo_file, self.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 merge_vcf_files(sample_files, cores, config): out_file = config["outputs"]["merge"] config["algorithm"] = {} run_parallel = parallel_runner({"type": "local", "cores": min(cores, 8)}, {}, config) vcfutils.parallel_combine_variants(sample_files, out_file, config["ref"]["GRCh37"], config, run_parallel) return out_file
def merge_vcf_files(sample_files, cores, config): out_file = config["outputs"]["merge"] config["algorithm"] = {} run_parallel = parallel_runner({ "type": "local", "cores": min(cores, 8) }, {}, config) vcfutils.parallel_combine_variants(sample_files, out_file, config["ref"]["GRCh37"], config, run_parallel) return out_file
def test_1_parallel_vcf_combine(self): """Parallel combination of VCF files, split by chromosome. """ var_dir = os.path.join(self.data_dir, "variants") files = [os.path.join(var_dir, "S1-variants.vcf"), os.path.join(var_dir, "S2-variants.vcf")] out_file = os.path.join(var_dir, "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")) run_parallel = parallel_runner({"type": "local", "cores": 1}, {}, config) region_dir = os.path.join(var_dir, "S1_S2-combined-regions") if os.path.exists(region_dir): shutil.rmtree(region_dir) if os.path.exists(out_file): os.remove(out_file) vcfutils.parallel_combine_variants(files, out_file, ref_file, config, run_parallel)
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") config = load_config(os.path.join(self.data_dir, "automated", "post_process-sample.yaml")) run_parallel = parallel_runner({"type": "local", "cores": 1}, {}, config) 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) 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_1_parallel_vcf_combine(self): """Parallel combination of VCF files, split by chromosome. """ # Be back compatible with 0.7.6 -- remove after 0.7.7 release if prun is None: return 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") config = load_config(os.path.join(self.data_dir, "automated", "post_process-sample.yaml")) 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")