def get_coords(data): for category, vtypes in [("LOH", {"LOSS", "HETEROZYGOSITY"}), ("amplification", {"AMPLIFICATION"})]: out = tz.get_in([category, dd.get_genome_build(data)], _COORDS, {}) priority_file = dd.get_svprioritize(data) if priority_file and os.path.basename(priority_file).find("civic") >= 0: for chrom, start, end, gene in _civic_regions(priority_file, vtypes, dd.get_disease(data)): out[gene] = (chrom, start, end) yield category, out
def get_coords(data): """Retrieve coordinates of genes of interest for prioritization. Can read from CIViC input data or a supplied BED file of chrom, start, end and gene information. """ for category, vtypes in [("LOH", {"LOSS", "HETEROZYGOSITY"}), ("amplification", {"AMPLIFICATION"})]: out = tz.get_in([category, dd.get_genome_build(data)], _COORDS, {}) priority_file = dd.get_svprioritize(data) if priority_file: if os.path.basename(priority_file).find("civic") >= 0: for chrom, start, end, gene in _civic_regions(priority_file, vtypes, dd.get_disease(data)): out[gene] = (chrom, start, end) elif os.path.basename(priority_file).find(".bed") >= 0: for line in utils.open_gzipsafe(priority_file): parts = line.strip().split("\t") if len(parts) >= 4: chrom, start, end, gene = parts[:4] out[gene] = (chrom, int(start), int(end)) yield category, out
def get_coords(data): """Retrieve coordinates of genes of interest for prioritization. Can read from CIViC input data or a supplied BED file of chrom, start, end and gene information. """ for category, vtypes in [("LOH", {"LOSS", "HETEROZYGOSITY"}), ("amplification", {"AMPLIFICATION"})]: out = tz.get_in([category, dd.get_genome_build(data)], _COORDS, {}) priority_file = dd.get_svprioritize(data) if priority_file: if os.path.basename(priority_file).find("civic") >= 0: for chrom, start, end, gene in _civic_regions( priority_file, vtypes, dd.get_disease(data)): out[gene] = (chrom, start, end) elif os.path.basename(priority_file).find(".bed") >= 0: for line in utils.open_gzipsafe(priority_file): parts = line.strip().split("\t") if len(parts) >= 4: chrom, start, end, gene = parts[:4] out[gene] = (chrom, int(start), int(end)) yield category, out