def rnaseq_variant_calling(samples, run_parallel): """ run RNA-seq variant calling using GATK """ samples = run_parallel("run_rnaseq_variant_calling", samples) variantcaller = dd.get_variantcaller(to_single_data(samples[0])) if variantcaller and ("gatk-haplotype" in variantcaller): out = [] for d in joint.square_off(samples, run_parallel): out.extend( [[to_single_data(xs)] for xs in multi.split_variants_by_sample(to_single_data(d))]) samples = out if variantcaller: samples = run_parallel("run_rnaseq_ann_filter", samples) if variantcaller and ("gatk-haplotype" in variantcaller): out = [] for data in (to_single_data(xs) for xs in samples): if "variants" not in data: data["variants"] = [] data["variants"].append({ "variantcaller": "gatk-haplotype", "vcf": data["vrn_file_orig"], "population": { "vcf": data["vrn_file"] } }) data["vrn_file"] = data.pop("vrn_file_orig") out.append([data]) samples = out return samples
def rnaseq_variant_calling(samples, run_parallel): """ run RNA-seq variant calling using GATK """ samples = run_parallel("run_rnaseq_variant_calling", samples) variantcaller = dd.get_variantcaller(to_single_data(samples[0])) if variantcaller and ("gatk-haplotype" in variantcaller): out = [] for d in joint.square_off(samples, run_parallel): out.extend([[to_single_data(xs)] for xs in multi.split_variants_by_sample(to_single_data(d))]) samples = out samples = run_parallel("run_rnaseq_ann_filter", samples) return samples
def rnaseq_variant_calling(samples, run_parallel): """ run RNA-seq variant calling using GATK """ samples = run_parallel("run_rnaseq_variant_calling", samples) variantcaller = dd.get_variantcaller(to_single_data(samples[0])) if variantcaller and ("gatk-haplotype" in variantcaller): out = [] for d in joint.square_off(samples, run_parallel): out.extend([[to_single_data(xs)] for xs in multi.split_variants_by_sample(to_single_data(d))]) samples = out if variantcaller: samples = run_parallel("run_rnaseq_ann_filter", samples) if variantcaller and ("gatk-haplotype" in variantcaller): out = [] for data in (to_single_data(xs) for xs in samples): if "variants" not in data: data["variants"] = [] data["variants"].append({"variantcaller": "gatk-haplotype", "vcf": data["vrn_file_orig"], "population": {"vcf": data["vrn_file"]}}) data["vrn_file"] = data.pop("vrn_file_orig") out.append([data]) samples = out return samples
def split_variants_by_sample(*args): return multi.split_variants_by_sample(*args)
def split_variants_by_sample(*args): return multi.split_variants_by_sample(*args)