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 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)